Transgenic plants with enhanced agronomic traits

ABSTRACT

This invention provides recombinant DNA constructs, transgenic plant nuclei and cells with such recombinant DNA construct for expression of proteins that are useful for imparting enhanced agronomic trait(s) to transgenic crop plants. This invention also provides transgenic plants and progeny seed comprising the transgenic plant cells where the plants are selected for having an enhanced trait selected from the group of traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Also disclosed are methods for manufacturing transgenic seed and plants with enhanced traits.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 14/998,728, filed Feb. 8, 2016, which application is a continuation of U.S. application Ser. No. 13/815,411, filed Feb. 27, 2013, which application is a continuation of U.S. application Ser. No. 12/218,251, filed Jul. 10, 2008, which application claims the benefit of priority under 35 USC § 119(e) of U.S. provisional application Ser. No. 60/958,909, filed Jul. 10, 2007, the contents of which are incorporated by reference in their entireties.

INCORPORATION OF SEQUENCE LISTING

Two copies of the sequence listing (Copy 1 and Copy 2) and a computer readable form (CRF) of the sequence listing, all on CD-Rs, each containing the text file named “3126.026US3 seq list text (1545469x7ADA8).TXT”, which is 105,787,392 bytes (measured in MS-Windows), were created on Feb. 11, 2016 and are herein incorporated by reference.

INCORPORATION OF COMPUTER PROGRAM LISTING

Two copies of the Computer Program Listing (Copy 1 and Copy 2) and a computer readable form (CRF) containing folders hmmer-2.3.2 and 226pfamdir, all on CD-Rs are incorporated herein by reference in their entirety. Folder Hmmer-2.3.2 contains the source code and other associated file for implementing the HMMer software for Pfam analysis. Folder 226pfamDir contains 226 Pfam Hidden Markov Models. Both folders were created on CD-R on Dec. 5, 2017, having a total size of 19,449,856 bytes (measured in MS-WINDOWS).

FIELD OF THE INVENTION

Disclosed herein are recombinant DNA useful for providing enhanced traits to transgenic plants, seeds, pollen, plant cells and plant nucleui of such transgenic plants, methods of making and using such recombinant DNA, plants, seeds, pollen, plant cells and plant nuclei. Also disclosed are methods of producing hybrid seed comprising such recombinant DNA.

SUMMARY OF THE INVENTION

This invention employs recombinant DNA for expression of proteins that are useful for imparting enhanced agronomic traits to the transgenic plants. Recombinant DNA in this invention is provided in a construct comprising a promoter that is functional in plant cells and that is operably linked to a DNA segment that encodes a protein. In some embodiments of the invention, such protein defined by protein domains e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 11. In other embodiments of the invention, e.g. where a Pfam domain module is not available, such protein is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 30526 through SEQ ID NO: 30550. In more specific embodiments of the invention the protein expressed in plant cells is a protein selected from the group of proteins identified in Table 2 and their homologs identified in Table 8.

Other aspects of the invention are specifically directed to plant cell nuclei and transgenic cells comprising the recombinant DNA construct of the invention, transgenic plants comprising a plurality of such plant cells, progeny transgenic seed, embryo and transgenic pollen from such plants. Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA construct and expressed the protein by screening transgenic plants in the population for an enhanced trait as compared to control plants that do not have the recombinant DNA construct, where the enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

In yet another aspect of the invention the plant cell nuclei, plant cells, transgenic plants, seeds, and pollen further comprise recombinant DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell. Such tolerance is especially useful not only as an advantageous trait in such plants but is also useful in a selection step in the methods of the invention. In aspects of the invention such herbicide is a glyphosate, dicamba, or glufosinate compound.

Yet other aspects of the invention provide transgenic plants which are homozygous for the recombinant DNA and transgenic seed of the invention from corn, soybean, cotton, canola, alfalfa, wheat or rice plants.

This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA construct provided by herein. More specifically the method comprises (a) screening a population of plants for an enhanced trait and a recombinant DNA construct of the invention, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA, (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants, and (c) collecting seed from a selected plant. The method further comprises (d) verifying that the recombinant DNA construct is stably integrated in said selected plants, and (e) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein selected from SEQ ID NO: 299 through SEQ ID NO: 30468. In one aspect of the invention the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to a herbicide applied at levels that are lethal to wild type plant cells and the selecting is affected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention the plants are selected by identifying plants with the enhanced trait. The methods are especially useful for manufacturing corn, soybean, cotton, canola, alfalfa, wheat or rice seed.

Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA construct comprising a promoter that is (a) functional in plant cells and (b) is operably linked to DNA that encodes a protein provided by the invention. The methods further comprise producing corn plants from the hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for the recombinant DNA construct, and a fraction of the plants produced from said hybrid corn seed has none of the recombinant DNA construct; selecting corn plants which are homozygous and hemizygous for the recombinant DNA construct by beating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting the seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a consensus amino acid sequence of SEQ ID NO: 301 and its homologs.

FIGS. 2-4 are plasmid maps.

DETAILED DESCRIPTION OF THE INVENTION

In the attached sequence listing:

SEQ ID NO:1-298 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, i.e. each represents a coding sequence for a protein;

SEQ ID NO: 299-596 are amino acid sequences of the cognate protein of the “genes” with nucleotide coding sequences 1-298;

SEQ ID NO: 597-30468 are amino acid sequences of homologous proteins;

SEQ ID NO: 30469-30520 are nucleotide sequences of the elements in base plasmid vectors SEQ ID NO: 30521 is a nucleotide sequence of a base plasmid vector useful for corn transformation;

SEQ ID NO: 30522 is a nucleotide sequence of a base plasmid vector useful for soybean and canola transformation;

SEQ ID NO: 30523 is a nucleotide sequence of a base plasmid vector useful for cotton transformation;

SEQ ID NO: 30524 is a nucleotide sequence of a Sphas1 promoter from soybean;

SEQ ID NO: 30525 is a nucleotide sequence of a Sphas1 leader from soybean.

SEQ ID NO: 30526-30550 are consensus sequences.

Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.

TABLE 1 Gene ID PEP SEQ ID NO Consensus SEQ ID NO PHE0006007_18714 301 30526 PHE0006460_15962 453 30527 PHE0006657_16192 334 30528 PHE0006712_16273 415 30529 PHE0006859_16873 376 30530 PHE0006907_16797 594 30531 PHE0006936_16828 348 30532 PHE0006969_16871 428 30533 PHE0007578_17852 446 30534 PHE0007650_18175 358 30535 PHE0008172_18471 397 30536 PHE0008308_18841 392 30537 PHE0008340_19155 410 30538 PHE0008422_18842 412 30539 PHE0008698_24421 364 30540 PHE0010197_21429 569 30541 PHE0010201_21433 576 30542 PHE0010201_21768 574 30543 PHE0010223_21491 545 30544 PHE0010397_21762 538 30545 PHE0010398_21763 539 30546 PHE0010615_22400 510 30547 PHE0010838_22702 575 30548 PHE0011447_23660 586 30549 PHE0012170_24424 572 30550

As used herein a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA construct, e.g. by Agrobacterium-mediated transformation or by bombardment using microparticles coated with recombinant DNA construct or other means. A plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.

As used herein a “transgenic plant” means a plant whose genome has been altered by the stable integration of recombinant DNA construct. A transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.

As used herein “recombinant DNA” means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.

As used herein “consensus sequence” means an artificial sequence of amino acids in a conserved region of an alignment of amino acid sequences of homologous proteins, e.g. as determined by a CLUSTALW alignment of amino acid sequence of homolog proteins.

As used herein a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention. Homologs are expressed by homologous genes. Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a polynucleotide useful in the present invention may have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 298 substitution in accordance with degeneracy of the genetic code. Homologs are proteins that, when optimally aligned, have at least 60% identity, more preferably about 70% or higher, more preferably at least 80% and even more preferably at least 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells. Homologs include proteins with an amino acid sequence that has at least 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.

Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. A local sequence alignment program, e.g. BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism may not necessarily be an ortholog or the only ortholog, a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. A further aspect of the invention comprises functional homolog proteins that differ in one or more amino acids from those of disclosed protein as the result of conservative amino acid substitutions, for example substitutions are among: acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; basic (positively charged) amino acids such as arginine, histidine, and lysine; neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; amino acids having aliphatic side chains such as glycine, alanine, valine, leucine, and isoleucine; amino acids having aliphatic-hydroxyl side chains such as serine and threonine; amino acids having amide-containing side chains such as asparagine and glutamine; amino acids having aromatic side chains such as phenylalanine, tyrosine, and tryptophan; amino acids having basic side chains such as lysine, arginine, and histidine; amino acids having sulfur-containing side chains such as cysteine and methionine; naturally conservative amino acids such as valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the homologs encoded by DNA useful in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.

“Percent identity” describes the extent to which the sequences of DNA or protein segments are invariant throughout a window of alignment of nucleotide or amino acid sequences. An “identity fraction” for a sequence aligned with a reference sequence is the number of identical components which are shared by the sequences, divided by a length of the window of alignment, wherein the length does not include gaps introduced by an alignment algorithm. “Percent identity” (“% identity”) is the identity fraction times 100. The alignment algorithm is preferably a local alignment algorithm, such as BLASTp. As used herein, sequences are “aligned” when the alignment produced by BLASTp has a minimal e-value.

“Pfam” database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments are useful for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.

Protein domains are identified by querying the amino acid sequence of a protein against Hidden Markov Models which characterize protein family domains (“Pfam domains”) using HMMER software, a current version of which is provided in the appended computer listing. A protein domain meeting the gathering cutoff for the alignment of a particular Pfam domain is considered to contain the Pfam domain.

A “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies. A Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function. The Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins. A Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.

Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software. Candidate proteins meeting the same Pfam domain module are in the protein family and have cognate DNA that is useful in constructing recombinant DNA for the use in the plant cells of this invention. Hidden Markov Model databases for use with HMMER software in identifying DNA expressing protein with a common Pfam domain module for recombinant DNA in the plant cells of this invention are also included in the appended computer listing.

The HMMER software and Pfam databases are version 19.0 and were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO: 299 through SEQ ID NO: 596. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 14 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits. The relevant Pfams modules for use in this invention, as more specifically disclosed below, are zf-CCCH, PALP, GAF::HisKA::HATPase_c, TPR_2::TPR_1::TPR_2::TPR_1::TPR_4::TPR_2::TPR_1, efhand::efhand, Spermine_synth, ELFV_dehydrog_N::ELFV_dehydrog, PFK, PAS_3::PAS_3::Pkinase, S1, GDC-P, SWIM, B12-binding::Radical_SAM, S1, LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, Chloroa_b-bind, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, WD40::WD40, YABBY, Ldh_1_N::Ldh_1_C, Sina, Na_H_antiport_1, ParBc, YABBY, Histone, Fe_bilin_red, Tryp_alpha_amyl, Pyr_redox_2::Thioredoxin, E2F_TDP, CN_hydrolase, YDG_SRA::Pre-SET::SET, APC8::TPR_1::TPR_1::TPR_1, Ras, tRNA_anti::tRNA-synt_2, Auxin_inducible, PGI, S1, Chloroa_b-bind, Bac_globin, Glyco_hydro_17, MGS, Spermine_synth, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Aa_trans, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase_Tyr, Gln-synt_N::Gln-synt_C, SAP18, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C, zf-C3HC4, eIF-1a, RPE65, PBP, Pkinase, AA_permease, F-box::LRR_1::LRR_2, zf-CCCH::zf-CCCH, Lactamase_B::Flavodoxin_1::Flavin_Reduct, Bac_globin, DSPc, adh_short, Tim17, Oxidored_molyb::Mo-co_dimer::Cyt-b5::FAD_binding_6::NAD_binding_1, ubiquitin::ubiquitin::ubiquitin::ubiquitin, MBD, CXC::CXC, HSF_DNA-bind, Spermine_synth, AP2, Peptidase_S10, PALP, EIN3, Gln-synt_N::Gln-synt_C, 2OG-FeII_Oxy, Glyco_hydro_9, GDC-P, B3, PTPA, Acyltransferase, Isochorismatase, FMO-like, Molybdop_Fe4S4::Molybdopterin::Molydop_binding::Fer2_BFD, Lir1, Prismane, Fer2, DEAD::Helicase_C, Molybdop_Fe4S4::Molybdopterin::Molydop_binding::Fer2_BFD, KNOX1::KNOX2::ELK, Glyoxalase, Sad1_UNC, Bac_globin, VPS28, PP2C, Pkinase::efhand::efhand::efhand, LEA_3, Peptidase_S10, Pkinase, CBFD_NFYB_HMF, Gln-synt_N::Gln-synt_C, Pyr_redox_2::Fer2_BFD::NIR_SIR_ferr:NIR_SIR, NUDIX::NUDIX, FAD_binding_3, GST_N::GST_C, SAM_decarbox, Acyltransferase, NTP_transferase, G-patch, 2OG-FeII_Oxy, Gln-synt_N::Gln-synt_C, AAA::Vps4_C, Histone, Pkinase, TPR_1, F-box::Kelch_1::Kelch_1, Spermine_synth, Bac_globin, Bac_globin, zf-UBR, Homeobox::HALZ, Whirly, NAD_binding_1, PTR2, EIN3, 4HBT, adh_short, 2OG-FeII_Oxy, P-II, Myb_DNA-binding::Myb_DNA-binding, DAGK_cat, AP2, MFS_1, Chloroa_b-bind, DUF716, zf-Dof, CCT, Homeobox::HALZ, Histone, 2OG-FeII_Oxy, Globin, Pyr_redox_2::Fer2_BFD::NIR_SIR_ferr:NIR_SIR, Whirly, PsbP, bZIP_1, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase_Tyr, Phil, BURP, Sterol_desat, DSPc, SNF5, Acyltransferase, GATase_2::Asn_synthase, adh_short, Homeobox::START, Pkinase, ParBc, SOI1L, DNA_photolyase::FAD_binding_7, Pkinase_Tyr, NAD_Gly3P_dh_N::NAD_Gly3P_dh_C, Na_H_Exchanger, peroxidase, Oxidored_molyb::Mo-co_dimer::Cyt-b5::FAD_binding_6::NAD_binding_1, Hexokinase_1::Hexokinase_2, DUF716, S10_plectin, Thi4, p450, CCT, adh_short, PSI_PSAK, DUF640, Thioredoxin, Globin, Ank::Pkinase, DAGAT, RPE65, Ank::Pkinase, GSHPx, Gln-synt_N::Gln-synt_C, MtN3_slv::MtN3_slv, Allene_ox_cyc, IGPD, MBD, CorA, Response_reg, Histone, AAA, Ribosomal_L10e, Pkinase, DUF26::DUF26::Pkinase, p450, mTERF, AA_kinase, PBP, GUN4, Lactamase_B::Flavodoxin_1::Rubredoxin, C2, RRM_1::RRM_1, Histone, Alpha-amylase, HLH, Thioredoxin, Histone_HNS, Myb_DNA-binding::Myb_DNA-binding, Cytochrom_C552, AP2::AP2, MtN3_slv::MtN3_slv, SHMT, ParBc, Mit_rib_S27, Ribosomal_S2, KNOX1::KNOX2::ELK, MFS_1, Glyco_transf_5::Glycos_transf_1, Cellulase, Ribosomal_L10e, Spermine_synth, Glyco_hydro_2_N::Glyco_hydro_2::Glyco_hydro_2_C, TP_methylase, AP2::AP2, Histone, Response_reg::CCT, Histone_HNS, DUF1716, p450, GATA, Pkinase, Sugar_tr, Aa_trans, Pribosyltran, Ribosomal_L10e, HLH, PMSR, DnaJ::DnaJ_CXXCXGXG::DnaJ_C, DUF1005, Glyco_transf_5::Glycos_transf_1, Spermine_synth, S1::EIF_2_alpha, RGS, Na_sulph_symp, S1, MtN3_slv::MtN3_slv, Lactamase_B::Flavin_Reduct, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Chloroa_b-bind, PTR2, Agglutinin, PLATZ, NPH3, Auxin_inducible, PTR2, GAF::HisKA::Response_reg, PsbQ, GSH_synth_ATP, GATase_2::Asn_synthase, PHP, FtsJ, DUF6::TPT, Proteasome, PsbW_2, Glyco_hydro_9, NAD_binding_2::6 PGD, S1::EIF_2_alpha, Homeobox::START::MEKHLA, S1, Isoamylase_N::Alpha-amylase, E2F_TDP, and Rieske::PaO, for which the databases are included in the appended computer listing.

As used herein “promoter” means regulatory DNA for initializing transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells. Thus, plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Bradyrhizobium bacteria. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”. A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most conditions.

As used herein “operably linked” means the association of two or more DNA fragments in a DNA construct so that the function of one, e.g. protein-encoding DNA, is controlled by the other, e.g. a promoter.

As used herein “expressed” means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.

As used herein a “control plant” means a plant that does not contain the recombinant DNA that expressed a protein that impart an enhanced trait. A control plant is to identify and select a transgenic plant that has an enhance trait. A suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, i.e. devoid of recombinant DNA. A suitable control plant may in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.

As used herein an “enhanced trait” means a characteristic of a transgenic plant that includes, but is not limited to, an enhance agronomic trait characterized by enhanced plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance. In more specific aspects of this invention enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. In an important aspect of the invention the enhanced trait is enhanced yield including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions may include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability and high plant density. “Yield” can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.

Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare. For example, maize yield may be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture. Increased yield may result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that may or may not correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as may be manifest by an alterations in the ratios of seed components.

A subset of the nucleic molecules of this invention includes fragments of the disclosed recombinant DNA consisting of oligonucleotides of at least 15, preferably at least 16 or 17, more preferably at least 18 or 19, and even more preferably at least 20 or more, consecutive nucleotides. Such oligonucleotides are fragments of the larger molecules having a sequence selected from the group consisting of SEQ ID NO:1 through SEQ ID NO: 298, and find use, for example as probes and primers for detection of the polynucleotides of the present invention.

In some embodiments of the invention a constitutively active mutant, e.g. SEQ ID NO: 203, is constructed to achieve the desired effect. In other embodiments of the invention, a dominant negative gene is constructed to adversely affect the normal, wild-type gene product within the same cell.

DNA constructs are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait. Other construct components may include additional regulatory elements, such as 5′ leaders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.

Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens and the CaMV35S promoters from the cauliflower mosaic virus as disclosed in U.S. Pat. Nos. 5,164,316 and 5,322,938. Useful promoters derived from plant genes are found in U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Pat. No. 7,151,204, which discloses a maize chloroplast aldolase promoter and a maize aldolase (FDA) promoter, and U.S. Patent Application Publication 2003/0131377 A1, which discloses a maize nicotianamine synthase promoter, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.

In other aspects of the invention, preferential expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).

Furthermore, the promoters may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein may be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence. In some instances, these 5′ enhancing elements are introns. Particularly useful as enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.

In other aspects of the invention, sufficient expression in plant seed tissues is desired to affect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy et al. (1996) Plant Mol Biol. 31(6):1205-1216).

Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site. Well-known 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No. 6,090,627, incorporated herein by reference; 3′ elements from plant genes such as wheat (Triticum aesevitum) heat shock protein 17 (Hsp17 3′), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea (Pisum sativum) ribulose biphosphate carboxylase gene (rbs 3′), and 3′ elements from the genes within the host plant.

Constructs and vectors may also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference. For description of the transit peptide region of an Arabidopsis EPSPS gene useful in the present invention, see Klee, H. J. et al (MGG (1987) 210:437-442).

Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA construct can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides. Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos. 5,094,945; 5,627,061; 5,633,435 and 6,040,497 for imparting glyphosate tolerance; polynucleotide molecules encoding a glyphosate oxidoreductase (GOX) disclosed in U.S. Pat. No. 5,463,175 and a glyphosate-N-acetyl transferase (GAT) disclosed in U.S. Patent Application publication 2003/0083480 A1 also for imparting glyphosate tolerance; dicamba monooxygenase disclosed in U.S. Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance; a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtI) described in Misawa et al, (1993) Plant J. 4:833-840 and in Misawa et al, (1994) Plant J. 6:481-489 for norflurazon tolerance; a polynucleotide molecule encoding acetohydroxyacid synthase (AHAS, aka ALS) described in Sathasiivan et al. (1990) Nucl. Acids Res. 18:2188-2193 for imparting tolerance to sulfonylurea herbicides; polynucleotide molecules known as bar genes disclosed in DeBlock, et al. (1987) EMBO J. 6:2513-2519 for imparting glufosinate and bialaphos tolerance; polynucleotide molecules disclosed in U.S. Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance; polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for imparting pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. patents and patent application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance are disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.

Plant Cell Transformation Methods

Numerous methods for transforming chromosomes in a plant cell nucleus with recombinant DNA are known in the art and are used in methods of preparing a transgenic plant cell nucleus cell, and plant. Two effective methods for such transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); U.S. Pat. No. 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn); U.S. Pat. No. 6,153,812 (wheat) and U.S. Pat. No. 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola); U.S. Pat. No. 5,591,616 (corn); U.S. Pat. No. 6,384,301 (soybean), U.S. Pat. No. 7,026,528 (wheat) and U.S. Pat. No. 6,329,571 (rice), all of which are incorporated herein by reference. Transformation of plant material is practiced in tissue culture on a nutrient media, i.e. a mixture of nutrients that will allow cells to grow in vitro. Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.

In addition to direct transformation of a plant material with a recombinant DNA, a transgenic plant cell nucleus can be prepared by crossing a first plant having cells with a transgenic nucleus with recombinant DNA with a second plant lacking the trangenci nucleus. For example, recombinant DNA can be introduced into a nucleus from a first plant line that is amenable to transformation to transgenic nucleus in cells that are grown into a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line. A transgenic plant with recombinant DNA providing an enhanced trait, e.g. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers both traits. Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line. The progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g. marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait. Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line

In the practice of transformation DNA is typically introduced into only a small percentage of target plant cells in any one transformation experiment. Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes. Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or a herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers. Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA. Commonly used selective marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate (aroA or EPSPS). Examples of such selectable markers are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Selectable markers which provide an ability to visually identify transformants can also be employed, for example, a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.

Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, may be cultured in regeneration media and allowed to mature into plants. Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO₂, and 25-250 microeinsteins m⁻² s⁻¹ of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue, and plant species. Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn. The regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.

Transgenic Plants and Seeds

Transgenic plants derived from the plant cells of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and pollen of this invention. Such transgenic plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait. For efficiency a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events. Transgenic plants grown from transgenic seed provided herein have enhanced agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality. Of particular interest are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Table 2 provides a list of protein encoding DNA (“genes”) that are useful as DNA segment in a recombinant DNA construct for production of transgenic plants with enhanced agronomic trait, the elements of Table 2 are described by reference to:

“PEP SEQ ID NO” identifies an amino acid sequence from SEQ ID NO: 299 to 596. “NUC SEQ ID NO” identifies a DNA sequence from SEQ ID NO:1 to 298. “BV id” is a reference to the identifying number of base vectors in Table 3 used for construction of the transformation vectors of the recombinant DNA. Construction of plant transformation constructs is illustrated in Example 1. “Gene Name” denotes a common name for protein encoded by the recombinant DNA. “Annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit; “% id” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST (-F T) between the sequence of interest provided herein and the hit sequence in GenBank.

TABLE 2 NUC SEQ ID NO PEP SEQ ID NO Gene ID BV ID Gene Name e-value % id GenBank ID Annotation 1 299 PHE0007721_18998 21 Corn Homeotic  1.00E−152 77 123183 gb|AAP76321.1| homeobox protein knotted-1 transcription factor KNOTTED1 [Zea mays] 2 300 PHE0007756_18009 33 Arabidopsis 9-cis- 0 90 15231856 dbj|BAB01336.1| 9-cis- epoxycarotenoid epoxycarotenoid dioxygenase dioxygenase [Arabidopsis thaliana] 3 301 PHE0006007_18714 30 Arabidopsis nodulin  1.00E−105 86 79607902 ref|NP_974371.2|unknown MtN21 family protein protein [Arabidopsis thaliana] 4 302 PHE0004988_15925 13 Arabidopsis 0 100 18412567 gb|AAN71945.1| transport transport inhibitor response 1 inhibitor response TIR1, AtFBL1 protein [Arabidopsis thaliana] 5 303 PHE0007140_21771 30 Arabidopsis nodulin  1.00E−121 92 18421965 gb|AAM61405.1| MtN3 like MtN3 like protein-4 [Arabidopsis thaliana] 5 303 PHE0007140_22049 13 Arabidopsis nodulin  1.00E−121 92 18421965 gb|AAM61405.1| MtN3 like MtN3 like protein-4 [Arabidopsis thaliana] 6 304 PHE0006823_16403 13 Arabidopsis class 2 3.00E−85 100 15228313 gb|AAM65188.1| Non non-symbiotic hemoglobin symbiotic hemoglobin Hb2 [Arabidopsis thaliana] 7 305 PHE0007440_22555 18 Corn putative GTP-  1.00E−107 91 115462975 gb|AAS98506.1] GTP-binding binding protein Rab11 protein Rab11 [Oryza sativa (japonica cultivar-group)] 8 306 PHE0000206_22432 9 Corn CDPK kinase domain 0 87 115450483 sp|P53684|Calcium-dependent protein kinase, isoform 11 (CDPK 11) [Oryza sativa (japonica cultivar-group)] 9 307 PHE0000598_16824 9 Corn B1 regulatory 0 91 22195 emb|CAA40544.1| regulatory protein protein [Zea mays] 10 308 PHE0007590_17883 8 E. coli ribosomal 7.00E−33 56 118740922 ref|ZP_01588962.1 |ribosomal protein S1 domain 3 protein S1 [Enterobacter sp. 638] 11 309 PHE0007588_17881 8 E. Coli RNAse E S1 domain 2.00E−45 98 52695516 pdb|1SMX| the S1 domain of Rnase E from E. Coli (Native) 12 310 PHE0007592_17885 8 Yeast pre-mRNA 1.00E−40 98 6320850 gb|AAB64546.1| pre-mRNA splicing factor RNA splicing factor RNA helicase helicase S1 domain [Saccharomyces cerevisiae] 13 311 PHE0007587_17880 8 E. coli 7.00E−35 100 124525928 ref|ZP_01697933.1| Polyribonucleotide Polyribonucleotide nucleotidyltransferase nucleotidyltransferase [Escherichia coli B] 14 312 PHE0007624_17923 8 E. coli translation 8.00E−34 100 15800747 ref|NP_286761.1| translation initiation factor IF-1 initiation factor IF-1 [Escherichia coli O157:H7 EDL933] 15 313 PHE0007591_17884 8 E. coli ribosomal 2.00E−20 51 118068082 ref|ZP_01536336.1| ribosomal protein S1 domain 5 protein S1 [Serratia proteamaculans 568] 16 314 PHE0007623_17922 8 Arabidopsis N-  1.00E−172 100 18401429 gb|AAM63266.1| putative carbamoylputrescine amidohydrolase nitrilase [Arabidopsis thaliana] 17 315 PHE0007583_17871 6 Rice MtN3 homolog  1.00E−130 100 125526770 gb|EAY74884.1|hypothetical protein OsI_002731 [Oryza sativa (indica cultivar-group)] 18 316 PHE0006618_16146 13 Corn putative 4.00E−49 95 115442401 dbj|BAB63622.1| putative 40S ribosomal protein S10 ribosomal protein S10 [Oryza sativa (japonica cultivar-group)] 19 317 PHE0006791_16374 9 Arabidopsis  1.00E−120 83 15231674 sp|Q9LX31|GUN4_ARATH GUN4_ARATH Tetrapyrrole- Tetrapyrrole-binding protein, chloroplast binding protein precursor [Arabidopsis thaliana] 20 318 PHE0007620_17918 13 Arabidopsis 0 96 15223971 dbj|BAF01533.1| thylakoid- thylakoid ascorbate bound ascorbate peroxidase peroxidase [Arabidopsis thaliana] 21 319 PHE0006659_16195 13 Soy hypothetical  1.00E−112 49 125540608 gb|EAY87003.1|hypothetical protein protein OsI_008236 [Oryza sativa (indica cultivar-group)] 22 320 PHE0006662_16198 13 Ralstonia 1.00E−06 38 114582111 ref|XP_001161638.1| metallidurans hypothetical protein isoform 1 [Pan troglodytes] hypothetical protein 23 321 PHE0006274_15867 13 Corn Transcription 0 78 115487438 gb|ABA96515.1| Transcription factor E2Fb factor E2F[Oryza sativa (japonica cultivar-group)] 24 322 PHE0006637_16166 14 Corn ABI1 homolog  1.00E−145 78 115437928 ref|NP_001043415.1 |Os01g0583100 (Oryza sativa (japonica cultivar-group)] 25 323 PHE0006926_16815 13 Corn putative 1.00E−84 81 115440323 dbj|BAB63580.1| putative vacuolar protein vacuolar protein sorting 28 sorting-associated protein [Oryza sativa (japonica cultivar-group)] 26 324 PHE0006821_16402 13 Corn 1-aminocyclopropane-  1.00E−176 79 115448975 dbj|BAD16875.1| 1- 1-carboxylate deaminase aminocyclopropane-1- carboxylate deaminase [Oryza sativa (japonica cultivar-group)] 27 325 PHE0007687_18057 29 Arabidopsis 0 100 21536828 gb|AAM61160.1| cytochrome cytochrome P450 P450 homolog (Arabidopsis thaliana] 27 325 PHE0007687_18200 13 Arabidopsis 0 100 21536828 gb|AAM61160.1| cytochrome cytochrome P450 P450 homolog, [Arabidopsis thaliana] 28 326 PHE0007642_17999 29 Arabidopsis Non- 0 94 15231245 sp|O48963| Phototropin-1 phototropic (Root phototropism protein 1) hypocotyl protein 1 [Arabidopsis thaliana] 29 327 PHE0007677_18052 29 Arabidopsis 0 100 15239022 ref|NP_196694.1|oxidoreductase oxidoreductase [Arabidopsis thaliana] 29 327 PHE0007677_18179 13 Arabidopsis 0 100 15239022 ref|NP_196694.1|oxidoreductase oxidoreductase [Arabidopsis thaliana] 30 328 PHE0007644_18001 29 Arabidopsis receptor 0 88 15220455 ref|NP_176918.1| protein protein kinase serine/threonine kinase [Arabidopsis thaliana] 30 328 PHE0007644_18169 13 Arabidopsis receptor 0 88 15220455 ref|NP_176918.1| protein protein kinase serine/threonine kinase [Arabidopsis thaliana] 31 329 PHE0007640_17992 29 Soy magnesium  1.00E−165 80 92889086 gb|ABE89684.1| Mg2+ transporter mrs2-1-like transporter protein, CorA-like [Medicago truncatula] 32 330 PHE0007678_18053 29 Arabidopsis acyl-  1.00E−107 100 18399594 ref|NP_564457.1| acyl-CoA CoA thioesterase thioesterase [Arabidopsis thaliana] 32 330 PHE0007678_18180 13 Arabidopsis acyl-  1.00E−107 100 18399594 ref|NP_564457.1| acyl-CoA CoA thioesterase thioesterase [Arabidopsis thaliana] 33 331 PHE0007649_18006 29 Arabidopsis putative 0 99 42566072 ref|NP_191542.2| protein kinase/ ankyrin protein threonine kinase/protein-tyrosine kinase kinase [Arabidopsis thaliana] 34 332 PHE0006726_16298 25 Arabidopsis putative 0 97 15224586 gb|AAC20725.1| putative ARP2/3 protein ARP2/3 protein complex complex subunit p41 subunit p41 [Arabidopsis thaliana] 35 333 PHE0006218_8776 25 Arabidopsis 0 85 18405775 ref|NP_565954.1|disulfide thioredoxin-disulfide oxidoreductase/thioredoxin-disulfide reductase reductase (Arabidopsis thaliana] 36 334 PHE0006657_16192 13 Corn putative ATP- 2.00E−83 71 115462871 gb|AAV31386.1| putative ATP- binding protein binding protein [Oryza sativa (japonica cultivar-group)] 37 335 PHE0002554_17876 13 Corn Chlorophyll  1.00E−158 95 2326947 emb|CAA90681.1| Chlorophyll a/b-binding protein a/b-binding protein CP29 CP29 precursor precursor [Zea mays] 37 335 PHE0002554_23104 9 Corn Chlorophyll  1.00E−158 95 2326947 emb|CAA90681.1| Chlorophyll a/b-binding protein a/b-binding protein CP29 CP29 precursor precursor [Zea mays] 38 336 PHE0006807_16388 13 Corn transcription  1.00E−140 64 115484281 gb|ABG22372.1| CCT motif factor APRR9 like family protein (Oryza sativa (japonica cultivar-group)] 39 337 PHE0003359_8487 9 Corn dwf4-like 0 86 60677681 dbj|BAD90972.1| cytochrome protein P450 [Oryza sativa (japonica cultivar-group)] 40 338 PHE0006542_15785 9 Arabidopsis  1.00E−149 100 15234942 ref|NP_194243.1| protein- methionine sulfoxide methionine-S-oxide reductase reductase [Arabidopsis thaliana] 41 339 PHE0007622_17921 8 Arabidopsis 0 100 18419941 gb|AAF01311.1| spermine spermine synthase synthase [Arabidopsis thaliana] 42 340 PHE0007630_17956 3 Corn GA3ox1  1.00E−151 75 125544881 gb|EAY91020.1|hypothetical protein OsI_012253 [Oryza sativa (indica cultivar-group)] 43 341 PHE0007593_17886 8 Corn spermidine  1.00E−169 92 115471679 dbj|BAD30581.1| spermidine synthase synthase 1 [Oryza sativa (japonica cultivar-group)] 44 342 PHE0006475_15588 9 Arbidopsis 9.00E−89 100 42571459 ref|NP_973820.1| calcium ion PsbQ_like binding (Arabidopsis thaliana] 45 343 PHE0007619_17915 13 Soy methyl-CpG- 1.00E−44 43 18394229 ref|NP_563971.1|MBD10; DNA binding domain- binding [Arabidopsis thaliana] containing protein 46 344 PHE0006846_16447 13 Soy cuticle protein 0 70 9758349 dbj|BAB08850.1| lipid transfer protein; glossy1 homolog [Arabidopsis thaliana] 47 345 PHE0007584_17874 13 Arabidopsis methyl-  1.00E−124 65 18394229 ref|NP_563971.1 |MBD10; CpG-binding DNA binding [Arabidopsis domain-containing protein thaliana] 48 346 PHE0003695_17913 17 Arabidopsis Erecta 0 95 15225286 gb|AAC49302.1| ERECTA, receptor protein kinase [Arabidopsis thaliana] 48 346 PHE0011554_23650 32 Arabidopsis Erecta 0 95 15225286 gb|AAC49302.1| ERECTA, receptor protein kinase [Arabidopsis thaliana] 49 347 PHE0003695_17879 8 Arabidopsis Erecta 0 95 15225286 gb|AAK59615.1| receptor protein kinase, ERECTA [Arabidopsis thaliana] 49 347 PHE0003695_23448 22 Arabidopsis Erecta 0 95 15225286 gb|AAK59615.1| receptor protein kinase, ERECTA [Arabidopsis thaliana] 50 348 PHE0006936_16828 29 Soy GNS1/SUR4 2.00E−91 66 92868497 gb|ABE78502.1|GNS1/SUR4 membrane protein membrane protein [Medicago truncatula] 51 349 PHE0007645_18002 29 Soy DNA binding 2.00E−26 32 21617964 gb|AAM67014.1| DNA binding protein protein-like [Arabidopsis thaliana] 52 350 PHE0006784_16366 6 Corn cysteine  1.00E−165 93 2829688 emb|CAA59798.1| O- synthase acetylserine (thiol) lyase; cysteine synthase [Zea mays] 53 351 PHE0006171_16491 13 Sorghum bicolor 6.00E−91 86 115463027 ref|NP_001055113.1|Os05g0295800 Glyoxalase [Oryza sativa (japonica cultivar-group)] 54 352 PHE0006868_16682 13 Arabidopsis 3.00E−05 100 21592593 gb|AAM64542.1| unknown ME01451 [Arabidopsis thaliana] 55 353 PHE0006906_16796 13 Corn 20S  1.00E−121 96 115480019 dbj|BAA28276.1| beta 6 proteasome subunit subunit of 20S proteasome beta-6 [Oryza sativa (japonica cultivar-group)] 56 354 PHE0006649_16180 13 Wheat putative DRE 5.00E−62 64 60547461 gb|AAX23704.1|HvCBF7 binding factor 2 [Hordeum vulgare subsp. vulgare] 57 355 PHE0006809_16390 13 E. coli hydroxylamine 0 97 89107724 ref|NP_415394.4| reductase hydroxylamine reductase [Escherichia coli K12] 58 356 PHE0006918_16808 13 Corn putative 0 82 125571037 gb|EAZ12552.1|hypothetical dihydropyrimidine protein OsJ_002377 [Oryza dehydrogenase sativa (japonica cultivar- group)] 59 357 PHE0007813_18219 6 Rice MtN3 homolog  1.00E−119 86 115445683 dbj|BAD23335.1| putative NEC1 [Oryza sativa (japonica cultivar-group)] 60 358 PHE0007650_18175 13 Arabidopsis Kin17 protein 0 83 18405389 AAD10649.1| Kin17 protein [Arabidopsis thaliana] 61 359 PHE0006825_16405 13 E. coli cytochrome c 0 100 15834306 ref|ZP_01699144.1| Nitrite nitrite reductase reductase [Escherichia coli B] 62 360 PHE0006964_16864 9 Corn asparaginyl- 0 84 115436616 dbj|BAB61140.1| putative tRNA synthetase asparagine-tRNA ligase [Oryza sativa (japonica cultivar-group)] 62 360 PHE0006964_16865 13 Corn asparaginyl- 0 84 115436616 dbj|BAB61140.1| putative tRNA synthetase asparagine-tRNA ligase [Oryza sativa (japonica cultivar-group)] 63 361 PHE0008105_18407 13 Yeast transcriptional  1.00E−116 88 6324934 sp|Q02516| Transcriptional activator HAP5 activator HAP5 [Saccharomyces cerevisiae] 63 361 PHE0008105_18733 30 Yeast transcriptional  1.00E−116 88 6324934 sp|Q02516| Transcriptional activator HAP5 activator HAP5 [Saccharomyces cerevisiae] 64 362 PHE0006630_16159 13 Corn malate 0 92 126888 sp|P15719 |MDHP_maize dehydrogenase Malate dehydrogenase [NADP] 65 363 PHE0006966_16868 29 Arabidopsis 0 95 18413170 ref|NP_567341.1|Cryptochrome Cryptochrome 1 1 [Arabidopsis thaliana] 66 364 PHE0008698_24421 3 Corn expressed 9.00E−06 38 115484935 gb|AAX96767.1| expressed protein protein [Oryza sativa (japonica cultivar-group)] 67 365 PHE0006608_16123 25 Soy glutathione 2.00E−82 90 21068666 emb|CAD31839.1|putative peroxidase phospholipid hydroperoxide glutathione peroxidase [Cicer arietinum] 68 366 PHE0010462_21459 na Deinococcus  1.00E−155 86 15805358 ref|NP_294052.1|MutT/nudix radiodurans family protein [Deinococcus nudixhydrolase radiodurans R1] 69 367 PHE0009211_21774 30 Arabidopsis 5.00E−50 89 15236198 ref|NP_195205.1|unknown PF02519-auxin protein [Arabidopsis thaliana] inducible-3 70 368 PHE0006256_8775 27 Arabidopsis 9-cis- 0 92 15231856 dbj|BAB01336.1| 9-cis- epoxycarotenoid dioxygenase epoxycarotenoid dioxygenase [Arabidopsis thaliana] 71 369 PHE0006989_16918 29 Arabidopsis putative 0 79 15231840 dbj|BAB01042.1| protein protein kinase kinase [Arabidopsis thaliana] 72 370 PHE0007649_18166 13 Arabidopsis putative 0 100 42566072 ref|NP_191542.2| protein ankyrin protein kinase kinase/serine/threonine kinase/ tyrosine kinase [Arabidopsis thaliana] 73 371 PHE0006708_16264 29 Soy DNA helicase 45 0 89 3097266 emb|CAA76677.1| translation initiation factor [Pisum sativum] 74 372 PHE0001117_19094 4 Corn transcription  1.00E−101 84 125527033 gb|EAY75147.1|hypothetical factor G1543-like protein OsI_002994 [Oryza sativa (indica cultivar-group)] 74 372 PHE0001117_19095 9 Corn transcription  1.00E−101 84 125527033 gb|EAY75147.1|hypothetical factor G1543-like protein OsI_002994 [Oryza sativa (indica cultivar-group)] 75 373 PHE0006266_8814 9 Corn phytochromobilin  1.00E−164 100 49472889 gb|AAT66259.1| synthase phytochromobilin synthase [Zea mays] 75 373 PHE0006266_15483 4 corn phytochromobilin  1.00E−164 100 49472889 gb|AAT66259.1| synthase phytochromobilin synthase [Zea mays] 76 374 PHE0006795_16378 13 E. coli pH-  1.00E−172 82 16128013 ref|NP_414560.1| pH- dependent sodium/proton dependent sodium/proton antiporter antiporter [Escherichia coli K12] 77 375 PHE0006956_16853 13 Agrobacterium 0 98 15891062 ref|NP 356734.1|hypothetical nitrate reductase protein AGR_L_1895 [Agrobacterium tumefaciens str. C58] 78 376 PHE0006859_16873 9 Corn bHLH protein family 2.00E−31 92 115451023 gb|EAZ25749.1| hypothetical protein OsJ_009232 [Oryza sativa (japonica cultivar-group)] 79 377 PHE0006824_16404 13 Corn Nonlegume 6.00E−86 98 3913789 gb|AAA19576.1| haemoglobin hemoglobin-like apoprotein [Hordeum vulgare] 80 378 PHE0006812_16393 13 Nostoc 2-on-2 1.00E−61 100 23130505 ref|ZP_00112318.1| Truncated hemoglobin hemoglobins (Nostoc punctiforme PCC 73102] 81 379 PHE0006815_16396 13 Rice Trb-like 2.00E−98 100 115468746 dbj|BAD32857.1| putative 2- on-2 hemoglobin [Oryza sativa (japonica cultivar-group)] 82 380 PHE0006806_16387 13 Corn Trb-like 7.00E−80 83 14165165 gb|AAK55410.1|AF376063_12- on-2 hemoglobin [Hordeum vulgare] 83 381 PHE0006624_16153 13 Corn putative 0 98 3342802 gb|AAC27703.1| putative cytosolic 6-phosphogluconate cytosolic 6-phosphogluconate dehydrogenase dehydrogenase [Zea mays] 84 382 PHE0005006_15823 13 Corn chlorophyll a/b-  1.00E−112 80 115458738 gb|EAY94374.1| hypothetical binding apoprotein protein OsI_015607 [Oryza CP24 precursor sativa (indica cultivar-group)] 85 383 PHE0003991_16771 13 Corn AfMONFEED000559 — — — — Protamine P1 86 384 PHE0006683_16229 13 Corn response  1.00E−102 85 12060384 dbj|BAB20579.1| response regulator 4 regulator 4 [Zea mays] 87 385 PHE0006884_16703 7 Corn granule-bound 0 89 33321047 gb|AAQ06291.1| granule- starch synthase precursor bound starch synthase precursor [Zea mays] 88 386 PHE0006691_16237 3 E. coli NAD(P)H- 0 100 15804152 ref|NP_290191.1| NAD(P)H- dependent glycerol- dependent glycerol-3-phosphate dehydrogenase 3-phosphate dehydrogenase [Escherichia coli O157:H7 EDL933] 89 387 PHE0006790_16372 9 Arabidopsis 0 95 15219408 ref|NP_175088.1| chlorophyll a chlorophyll A oxygenase [Arabidopsis oxygenase thaliana] 90 388 PHE0009143_19932 30 E. coli StpA 2.00E−57 86 83569970 ref|ZP_00921418.1| DNA- binding protein H-NS [Shigella dysenteriae 1012] 91 389 PHE0008406_18830 30 Yeast general amino 0 98 14318464 sp|P43548| Yeast general acid permease amino acid permease AGP3 92 390 PHE0008279_18708 30 Corn hypothetical 5.00E−25 73 115462095 gb|EAY96551.1| hypothetical protein protein OsI_017784 [Oryza sativa (indica cultivar-group)] 93 391 PHE0009142_19931 30 E. coli DNA-binding 3.00E−45 72 15801465 ref|NP_415753.1| global DNA- protein H-NS binding transcriptional dual regulator H-NS [Escherichia coli K12] 94 392 PHE0008308_18841 30 Corn hypothetical 5.00E−41 89 125537055 gb|EAY83543.1| hypothetical protein protein OsI_037502 [Oryza sativa (indica cultivar group)] 95 393 PHE0007639_17991 29 Chlorella optimized 0 99 118546 emb|CAA41636.1| glutamate beta glutamate dehydrogenase (NADP+) dehydrogenase [Chlorella sorokiniana] 96 394 PHE0007646_18170 13 Arabidopsis kelch repeat-containing 0 94 116831441 gb|ABK28673.1| unknown F-box family protein [Arabidopsis thaliana] 97 395 PHE0007765_18182 13 Arabidopsis  1.00E−130 100 15218872 ref|NP_176178.1| glutathione glutathione transferase transferase [Arabidopsis thallana] 98 396 PHE0008167_18465 5 Arabidopsis protein  1.00E−163 95 15233846 ref|NP_194179.1| protein kinase kinase/serine/threonine kinase/ protein-tyrosine kinase [Arabidopsis thaliana] 99 397 PHE0008172_18471 5 Arabidopsis putative 2.00E−46 97 4895214 gb|AAD32800.1| putative thioredoxin H thioredoxin H [Arabidopsis thaliana] 100 398 PHE0008183_18479 5 Arabidopsis 0 98 15239123 ref|NP_201371.1| protein receptor protein serine/threonine kinase kinase [Arabidopsis thaliana] 101 399 PHE0007585_17875 6 Arabidopsis drought- 2.00E−42 87 469112 emb|CAA55322.1| Di21 induced protein (Di21) [Arabidopsis thaliana] 101 399 PHE0007585_23902 30 Arabidopsis drought- 2.00E−42 87 469112 emb|CAA55322.1| Di21 induced protein (Di21) [Arabidopsis thaliana] 102 400 PHE0006804_16385 6 Rice small subunit of  1.00E−107 100 125553324 gb|EAY99033.1| hypothetical U2 snRNP auxiliary protein OsI_020266 [Oryza factor sativa (indica cultivar-group)] 103 401 PHE0006703_15751 15 Lactobacillus ATP-  1.00E−164 92 104773899 ref|YP_618879.1| 6- dependent phosphofructokinase phosphofructokinase [Lactobacillus delbrueckii with ctp subsp. bulgaricus ATCC 11842] 104 402 PHE0007410_17653 3 Umbelopsis glycerol-  1.00E−144 42 58264662 ref|XP_569487.1| glycerol-3- 3-phosphate O- phosphate O-acyltransferase acyltransferase [Cryptococcus neoformans var. neoformans JEC21] 105 403 PHE0006854_16456 2 Corn kernel specific  1.00E−115 71 32330681 gb|AAP79887.1| yabby10 yabby protein [Zea mays] 106 404 PHE0007721_21293 19 Corn homeobox  1.00E−152 77 123183 gb|AAP76321.1| homeobox transcription factor transcription factor KNOTTED1 KNOTTED1 [Zea mays] 107 405 PHE0006563_15990 13 Wheat glutamine- 0 97 53680379 gb|AAU89392.1| glutamine- dependent asparagine dependent asparagine synthetase synthetase [Triticum aestivum] 107 405 PHE0006563_16140 9 Wheat glutamine- 0 97 53680379 gb|AAU89392.1| glutamine- dependent asparagine dependent asparagine synthetase synthetase [Triticum aestivum] 108 406 PHE0006619_16147 13 Corn Delta 1- 0 84 2081612 dbj|BAA19916.1| deltal- pyrroline-5- pyrroline-5-carboxylate carboxylate synthetase [Oryza sativa synthetase (japonica cultivar-group)] 109 407 PHE0006813_16394 13 Bacillus subtilis 1.00E−67 93 16078221 sp|O31607| Hemoglobin-like Hemoglobin-like protein yjbl (Truncated BHb) protein TrHb (trBHb) [Bacillus Subtilis] 110 408 PHE0006688_16234 13 Corn ribosomal  1.00E−131 99 11467185 sp|P16037| maize Chloroplast protein S2 30S ribosomal protein S2 111 409 PHE0006635_16164 13 E. coli methylglyoxal 9.00E−86 100 15800822 ref|NP_286838.1|methylglyoxal synthase synthase [Escherichia coli O157:H7 EDL933] 112 410 PHE0008340_19155 30 Soy hypothetical  1.00E−178 78 92896427 gb|ABE93200.1| conserved protein hypothetical protein [Medicago truncatula] 113 411 PHE0008416_18838 30 Corn putative 0 58 115480880 ref|NP_001064033.1|Os10g01 oligopeptide 10600 [Oryza sativa (japonica transporter cultivar-group)] 114 412 PHE0008422_18842 30 Corn unknown  1.00E−121 55 115448163 dbj|BAD08083.1| unknown protein protein (Oryza sativa (japonica cultivar-group)] 115 413 PHE0008599_19166 30 Synechocystis 0 95 16330244 ref|NP_440972.1| glycogen glycogen operon operon protein; GlgX protein [Synechocystis sp. PCC 6803] 116 414 PHE0008375_18732 30 Bacillus 6.00E−95 99 16077136 sp|P37472| Hypoxanthine- hypoxanthine-guanine guanine phosphoribosyl-transferase phosphoribosyl-transferase (HGPRTase) [Bacillus subtilis] 117 415 PHE0006712_16273 27 Arabidopsis 4.00E−92 100 15237778 ref|NP_2007001.1| unknown unknown function protein [Arabidopsis thaliana] 117 415 PHE0006712_16362 13 Arabidopsis 4.00E−92 100 15237778 ref|NP_200700.1| unknown unknown function protein [Arabidopsis thaliana] 117 415 PHE0006712_16363 9 Arabidopsis 4.00E−92 100 15237778 ref|NP_200700.1| unknown unknown function protein [Arabidopsis thaliana] 117 415 PHE0006712_16364 6 Arabidopsis 4.00E−92 100 15237778 ref|NP_200700.1| unknown unknown function protein [Arabidopsis thaliana] 118 416 PHE0008394_18763 9 Corn altered 0 97 121341 sp|P25462| Glutamine glutamine synthetase (Glutamate-- synthetase ammonia ligase) (GS2) [Zea mays] 119 417 PHE0008395_18764 9 Corn altered 0 97 121341 sp|P25462| Glutamine glutamine synthetase (Glutamate-- synthetase ammonia ligase) (GS2) [Zea mays] 120 418 PHE0008444_18846 3 Corn glutamine 0 100 112490284 dbj|BAA03430.1| glutamine synthetase1 synthetase [Zea mays] 121 419 PHE0006819_16400 13 Synechocystis A- 0 100 16331685 sp|Q55393| Diflavin type flavoproteins flavoprotein A 1 (SsATF573) (NADH:oxygen oxidoreductase) [Synechocystis sp. PCC 6803] 122 420 PHE0007417_17663 15 Corn EIL1 0 76 125543684 gb|EAY89823.1| hypothetical protein OsI_011056 [Oryza sativa (indica cultivar-group)] 123 421 PHE0008443_18845 13 Barley asparagine 0 97 13925886 gb|AAK49456.1| glutamine- synthetase1 dependent asparagine synthetase 1 [Hordeum vulgare subsp. vulgare] 124 422 PHE0006818_16399 13 E. coli 0 100 16130617 ref|AP003277.1|flavorubredoxin flavorubredoxin oxidoreductase [Escherichia coli W3110] 125 423 PHE0006579_16031 13 Corn thiazole 0 97 2501189 sp|Q41738| Thiazole biosynthetic enzyme biosynthetic enzyme 1-1, chloroplast precursor [Zea mays] 126 424 PHE0006808_16389 13 Rice transcription 0 97 115484281 gb|ABG22372.1| CCT motif factor APRR9 like family protein [Oryza sativa (japonica cultivar-group)] 127 425 PHE0008160_18460 5 Arabidopsis 0 100 15234062 ref|NP_195033.1| pyruvate pyruvate decarboxylase [Arabidopsis decarboxylase thaliana] 128 426 PHE0007571_17834 24 Soy 0 97 7799808 emb|CAB91078.1| homoglutathione homoglutathione synthetase synthetase [Glycine max] 129 427 PHE0007586_17877 13 Arabidopsis  1.00E−151 96 15225630 gb|AAD32843.1| putative Chlorophyll a-b chlorophyll a/b binding protein binding protein [Arabidopsis thaliana] 130 428 PHE0006969_16871 13 Rice hypothetical 4.00E−34 100 115451023 gb|EAZ25749.1| hypothetical protein protein OsJ_009232 [Oryza sativa (japonica cultivar-group)] 131 429 PHE0009729_21717 13 Arabidopsis bHLH 1.00E−91 89 30698765 gb|AAO64014.1| putative homeodomain leucine zipper protein [Arabidopsis thaliana] 132 430 PHE0006424_15520 9 photosystem II 3.00E−37 75 15224531 gb|AAM64951.1| photosystem reaction center II reaction center 6.1 KD 6.1 KD protein protein [Arabidopsis thaliana] 133 431 PHE0006392_15480 9 Corn PsbP 9.00E−99 84 115489108 gb|ABA98969.2| Thylakoid lumenal 21.5 kDa protein [Oryza sativa (japonica cultivar-group)] 134 432 PHE0006589_16093 13 Arabidopsis 3.00E−84 100 42563272 dbj|BAE99426.1| thioredoxin- thioredoxin-like like protein [Arabidopsis protein thaliana] 135 433 PHE0009258_21487 16 Arabidopsis sodium 0 87 15240448 ref|NP_198067.1|NHX1 proton exchanger1 (NA+/H+ EXCHANGER); sodium:hydrogen antiporter [Arabidopsis thaliana] 135 433 PHE0009258_20132 34 Arabidopsis sodium 0 87 15240448 ref|NP_198067.1|NHX1 proton exchanger1 (NA+/H+ EXCHANGER); sodium:hydrogen antiporter [Arabidopsis thaliana] 136 434 PHE0006680_16226 13 Corn flavanone 3-  1.00E−161 81 18057095 gb|AAL58118.1| putative hydroxylase flavanone 3-hydroxylase [Oryza sativa (japonica cultivar-group)] 137 435 PHE0006481_16072 13 Corn Os09g0570300  1.00E−145 81 115480783 ref|NP_001063985.1|Os09g0570300 homolog [Oryza sativa (japonica cultivar-group)] 138 436 PHE0006269_8820 23 Synechocystis 0 96 16329708 ref|NP_440436.1|hypothetical conserved protein slr2048 [Synechocystis tetratricopeptide sp. PCC 6803] repeat protein 138 436 PHE0006269_8821 9 Syntechocystis 0 96 16329708 ref|NP_440436.1|hypothetical conserved protein slr2048 [Synechocystis tetratricopeptide sp. PCC 6803] repeat protein 139 437 PHE0006783_16365 11 Brassica napus 0 97 31455393 emb|CAD92450.1|amino acid amino acid permease 6 [Brassica napus] permease 6 140 438 PHE0003151_18392 28 Soy aintegumenta 2  1.00E−141 47 38492172 gb|AAR22388.1| ANT-like protein [Nicotiana tabacum] 141 439 PHE0008272_18723 30 Arabidopsis heat 0 88 15220611 sp|Q9S7U5| Heat shock shock factor protein 5 transcription factor 5) (HSTF 5) [Arabidopsis thaliana] 142 440 PHE0008277_18706 30 Yeast chromatin 0 95 6323354 sp|Q06168| Chromatin structure remodeling structure remodeling complex complex protein SFH1 protein SFH1 [Saccharomyces cerevisiae] 143 441 PHE0008109_18411 30 Yeast uncharacterized 0 93 6324728 sp|Q12232| Yeast protein YOR154W precursor uncharacterized protein YOR154W precursor 143 441 PHE0008109_18568 13 Yeast uncharacterized 0 93 6324728 sp|Q12232| Yeast protein YOR154W precursor uncharacterized protein YOR154W precursor 144 442 PHE0008280_18826 30 Sinorhizobium 0 93 16263847 ref|NP_436639.1| putative putative trehalose trehalose synthase protein synthase [Sinorhizobium meliloti 1021] 145 443 PHE0002424_15825 13 Corn  1.00E−140 77 90398977 gb|EAY96061.1| hypothetical NADPH:protochloro- protein OsI_017294 [Oryza phyllide sativa (indica cultivar group)] oxidoreductase A 146 444 PHE0006914_16804 13 Corn 26S protease 0 100 115466876 dbj|BAD35266.1| 26S protease regulatory subunit 7 regulatory subunit 7 [Oryza sativa (japonica cultivar-group)] 147 445 PHE0006642_16172 14 Rice ent-kaurene 0 97 115468620 dbj|BAD54598.1| ent-kaurene oxidase oxidase [Oryza sativa (japonica cultivar-group)] 148 446 PHE0007578_17852 29 Arabidopsis 2.00E−71 100 18395285 ref|NP_564202.1|unknown unknown protein protein [Arabidopsis thaliana] 149 447 PHE0009926_21079 30 Arabidopsis putative 1.00E−84 100 18397475 gb|AAM62982.1| putative dual dual-specificity specificity protein phosphatase protein phosphatase [Arabidopsis thaliana] 150 448 PHE0006206_19159 30 Arabidopsis ubiquitin 0 97 15234306 ref|NP_194517.1 |ubiquitin- ligase SINAT5 protein ligase/zinc ion binding [Arabidopsis thaliana] 151 449 PHE0008274_18705 30 Arabidopsis putative  1.00E−154 95 15222103 gb|AAD43166.1| Putative BURP domain BURP domain containing containing protein protein [Arabidopsis thaliana] 152 450 PHE0009510_20526 30 Cucurbita  1.00E−164 89 49425361 gb|AAT66041.1| spermidine spermidine synthase synthase [Cucumis sativus] 153 451 PHE0009937_21097 34 Cucurbita  1.00E−164 89 49425361 gb|AAT66041.1| spermidine spermidine synthase synthase [Cucumis sativus] 154 452 PHE0009927_21080 30 Brassica putative 4.00E−79 88 30679726 dbj|BAC42108.1| putative dual- dual-specificity specificity protein phosphatase protein phosphatase [Arabidopsis thaliana] 155 453 PHE0006460_15962 13 Arabidopsis 0 86 18394658 ref|NP_564064.1|unknown unknown protein protein [Arabidopsis thaliana] 156 454 PHE0006445_15956 13 Arabidopsis allene  1.00E−142 100 18404656 emb|CAC83762.1| allene oxide oxide cyclase cyclase [Arabidopsis thaliana] 157 455 PHE0006987_16893 13 Arabidopsis  1.00E−125 99 15241101 dbj|BAB09281.1| calcineurin B- calcineurin B-like like protein 2 [Arabidopsis protein 2 thaliana] 158 456 PHE0004230_15865 13 Corn E2F3 like 0 72 115446539 dbj|BAD73815.1| putative E2F homolog [Oryza sativa (japonica cultivar-group)] 159 457 PHE0006814_16395 13 Arabidopsis 2-on-2 2.00E−99 100 18418064 dbj|BAD42999.1| 2-on-2 hemoglobin hemoglobin (GLB3) [Arabidopsis thaliana] 160 458 PHE0002773_15881 13 Rice glucose-1- 0 100 115465649 ref|NP_001056424.1|Os05g0580000 phosphate adenylyltransferase [Oryza sativa (japonica large subunit 1 cultivar-group)] 161 459 PHE0006060_15842 13 Corn ubiquitin 0 86 60677681 dbj|BAD90972.1|cytochrome precursor P450 [Oryza sativa (japonica cultivar-group)] 162 460 PHE0006850_16451 2 Corn kernel specific 4.00E−73 74 115454365 dbj|BAF45803.1| YABBY2 yabby protein [Oryza sativa (japonica cultivar group)] 163 461 PHE0008043_18199 2 Corn homeobox-9 0 99 40950648 gb|AAR97952.1| rolled leaf1 [Zea mays] 164 462 PHE0000125_18852 13 Corn receiver  1.00E−171 73 51571875 dbj|BAD38854.1| pseudo- domain (TOC1-like) 10 response regulator 1 [Oryza sativa (japonica cultivar-group)] 165 463 PHE0008269_18720 30 Arabidopsis protein 0 96 15222311 ref|NP_172195.1|MAPKKK13; kinase protein kinase/protein serine/ threonine kinase/protein- tyrosine kinase [Arabidopsis thaliana] 166 464 PHE0008264_18712 30 Arabidopsis 0 97 42567081 ref|NP_194117.3| ubiquitin- ubiquitin-protein protein ligase/zinc ion binding ligase [Arabidopsis thaliana] 167 465 PHE0002782_20059 8 Corn 0 89 115479643 dbj|BAD17509.1| putative phosphoglucose glucose-6-phosphate isomerase isomerase [Oryza sativa (japonica cultivar group)] 167 465 PHE0002782_22452 13 Corn 0 89 115479643 dbj|BAD17509.1| putative phosphoglucose glucose-6-phosphate isomerase isomerase [Oryza sativa (japonica cultivar-group)] 168 466 PHE0009438_20404 9 Corn GNC 8.00E−84 52 115445073 dbj|BAD17612.1| zinc finger protein-like [Oryza sativa (japonica cultivar-group)] 169 467 PHE0009429_20392 13 Rice sulphiredoxin 6.00E−68 85 71905635 gb|AAZ52795.1| sulfiredoxin- like protein [Oryza sativa (japonica cultivar-group)] 170 468 PHE0009440_20406 13 Yeast sulphiredoxin 3.00E−66 100 6322764 sp|P36077|SRX1_YEAST Sulfiredoxin 171 469 PHE0008543_18945 13 Agrobacterium 0 97 17937602 ref|NP_534391.1| siroheme siroheme synthase synthase [Agrobacterium tumefaciens str. C58] 171 469 PHE0008543_18946 20 Agrobacterium 0 97 17937602 ref|NP_534391.1| siroheme siroheme synthase synthase [Agrobacterium tumefaciens str. C58] 171 469 PHE0008543_18947 10 Agrobacterium 0 97 17937602 ref|NP_534391.1| siroheme siroheme synthase synthase [Agrobacterium tumefaciens str. C58] 172 470 PHE0006960_16857 8 Rice nitrate 0 96 115448947 dbj|BAD16843.1| putative reductase nitrate reductase [Oryza sativa (japonica cultivar-group)] 173 471 PHE0009427_20389 13 Arabidopsis  1.00E−118 88 30686639 dbj|BAB01781.1| imidazoleglycerol- imidazoleglycerol-phosphate phosphate dehydratase [Arabidopsis dehydratase thaliana] 174 472 PHE0006437_15906 13 Arabidopsis putative  1.00E−170 95 22327062 ref|NP_197926.2| protein protein kinase kinase/protein serine/ threonine kinase/protein- tyrosine kinase [Arabidopsis thaliana] 175 473 PHE0007409_17652 3 Rice mono- or 0 99 115467862 dbj|BAD33251.1| putative diacylglycerol mono- or diacylglycerol acyltransferase acyltransferase (Oryza sativa (japonica cultivar-group)] 176 474 PHE0009426_20387 13 Yeast histidinol 0 100 14318548 dbj|BAA09264.1| histidinol phosphatase phosphatase [Saccharomyces cerevisiae] 177 475 PHE0009430_20393 13 Soy sulphiredoxin 2.00E−45 74 85719364 gb|ABC75369.1|ParB-like nuclease [Medicago truncatula] 178 476 PHE0007003_16906 13 Rice putative  1.00E−171 82 115467132 dbj|BAD37240.1| putative phosphotyrosyl phosphotyrosyl phosphatase phosphatase activator [Oryza sativa activator (japonica cultivar-group)] 179 477 PHE0008378_18741 13 Yeast general  1.00E−144 94 6320828 sp|P03069| General control control protein protein GCN4 (Amino acid biosynthesis regulatory protein) [Saccharomyces cerevisiae] 180 478 PHE0008273_18725 30 Arabidopsis nucleic 0 95 30683900 ref|NP_180412.2| nucleic acid acid binding protein binding [Arabidopsis thaliana] 181 479 PHE0008547_18953 20 Corn ferredoxin 1.00E−38 75 119961 sp|P27789| Maize ferredoxin-5 (Ferredoxin V) 182 480 PHE0006922_16812 13 Corn putative 0 87 115439869 gb|AAZ93623.1| hexokinase 6 hexokinase I [Oryza sativa (japonica cultivar-group)] 183 481 PHE0006920_16810 13 Corn putative CAD 0 88 115439215 gb|AAP92128.1| putative ATPase ATPase ATP1 [Oryza sativa (japonica cultivar-group)] 184 482 PHE0008396_18765 9 Corn altered 0 97 121341 sp|P25462| Maize glutamine glutamine synthetase (Glutamate-- synthetase2 ammonia ligase) (GS2) 185 483 PHE0006957_16854 13 Corn glutamine synthetase2 0 97 121341 sp|P25462| Maize glutamine C299A/C364A double mutant synthetase (Glutamate-- ammonia ligase) (GS2) 186 484 PHE0006404_15936 13 Arabidopsis RNA- 0 96 18423760 ref|NP_568826.1|RNA binding binding protein protein [Arabidopsis thaliana] 187 485 PHE0006820_16401 13 Nostoc punctiforme 0 97 23129576 ref|ZP_00111402.1|Uncharac- A-type flavoproteins terized flavoproteins [Nostoc punctiforme PCC 73102] 188 486 PHE0006690_16236 13 Corn putative high 0 79 108794607 gb|ABG20828.1| high affinity affinity nitrate nitrate transporter NRT2.5 transporter [Hordeum vulgare subsp. vulgare] 189 487 PHE0006395_15932 13 Arabidopsis leucine- 0 100 18391461 gb|AAW57412.1| plant rich repeat protein intracellular Ras-group-related LRR protein 3 [Arabidopsis thaliana] 190 488 PHE0006759_16384 6 Arabidopsis glycine 0 100 15235745 ref|NP_195506.1| Serine hydroxymethyltrans- hydroxymethyltransferase 1); ferase/serine glycine hydroxymethyl- hydroxymethyltransferase transferase [Arabidopsis thaliana] 191 489 PHE0006576_16028 13 Corn tuber-specific 1.00E−87 57 115469098 dbj|BAD37513.1| putative and sucrose-responsive element tuber-specific and sucrose-responsive element binding binding factor factor [Oryza sativa (japonica cultivar-group)] 192 490 PHE0006979_16885 13 Arabidopsis xylogen  1.00E−103 100 18405294 dbj|BAE73268.1| xylogen like like protein 12 protein 12 [Arabidopsis thaliana] 193 491 PHE0009786_21754 9 Arabidopsis HFR1- 1.00E−97 93 18378953 sp|Q9FE22| Long hypocotyl in delta N105 mutant far-red 1 (bHLH-like protein HFR1); gb|AAK15282.1 basic helix-loop-helix FB|1 protein [Arabidopsis thaliana] 193 491 PHE0009786_20911 30 Arabidopsis HFR1- 1.00E−97 93 18378953 sp|Q9FE22| Long hypocotyl in delta N105 mutant far-red 1 (bHLH-like protein HER1); gb|AAK10282.1 basic helix-loop-helix FB|1 protein [Arabidopsis thaliana] 194 492 PHE0006572_16007 13 Arabidopsis  1.00E−160 100 18396914 ref|NP_566229.1|Phosphoenol phosphoenolpyruvate pyruvate carboxylase kinase 2 carboxylase kinase 2 [Arabidopsis thaliana] 195 493 PHE0006828_16408 13 Arabidopsis de- 0 94 42566387 ref|NP_192756.2|DET1 (De- etiolated 1 etiolated 1) [Arabidopsis thaliana] 196 494 PHE0006588_16092 13 Corn electron 9.00E−90 100 30693659 ref|NP_175021.2 |electron transporter/thiol- transporter/thiol-disulfide disulfide exchange exchange intermediate intermediate [Arabidopsis thaliana] 197 495 PHE0006985_16891 13 Corn putative 0 75 115450034 dbj|BAD23003.1| putative nuclear protein NAP nuclear protein NAP [Oryza sativa (japonica cultivar-group)] 198 496 PHE0006875_16688 13 Rice putative Photosystem I 6.00E−61 85 115479799 dbj|BAD33396.1| putative reaction center subunit V photosystem I reaction center subunit V [Oryza sativa (japonica cultivar-group)] 199 497 PHE0006626_16155 13 Corn (1-3,1-4)-beta-  1.00E−134 72 18984 emb|CAA36801.1| (1-3,1-4)- glucanase beta-D-glucanase; emb|CAB41401.1| lichenase [Hordeum vulgare subsp. vulgare] 200 498 PHE0006689_16235 13 Corn amino acid 0 84 115443611 dbj|BAD08181.1| putative transporter family amino acid transport protein protein [Oryza sativa (japonica cultivar-group)] 201 499 PHE0006799_16382 9 Rhodopseudomonas 0 97 39934738 ref|NP 947014.1 |Mg- Mg-protoporphyrin protoporphyrin IX monomethyl IX monomethylester ester oxidative cyclase 66 kD cyclase subunit [Rhodopseudomonas palustris CGA009] 202 500 PHE0006959_16856 8 nitrate reductase 0 95 115476820 dbj|BAD09558.1| nitrate reductase apoenzyme [Oryza sativa (japonica cultivar- group)] 203 501 PHE0011615_23861 31 Arabidopsis 0 78 38049268 gb|AAR10436.1| YDA activated YODA [Arabidopsis thaliana] 204 502 PHE0006925_16814 13 Corn translocase 2.00E−74 66 115473245 dbj|BAC83874.1| translocase inner membrane-like inner membrane-like protein protein [Oryza sativa (japonica cultivar-group)] 205 503 PHE0006713_16274 25 Arabidopsis cell 0 96 15228343 emb|CAB51062.1| cell division division cycle protein 23-like cycle protein 23 homolog [Arabidopsis thaliana] 206 504 PHE0008447_18848 13 Corn light regulated 1.00E−23 63 77023866 gb|ABA61130.1| light-induced protein protein 1 [Lolium perenne] 207 505 PHE0006674_16221 13 Rice putative nitrate 0 95 115441781 dbj|BAD82445.1| putative transporter NRT1-5 nitrate transporter NRT1-5 [Oryza sativa (japonica cultivar-group)] 208 506 PHE0010613_22398 3 Corn high oil DAG  1.00E−165 80 115450433 gb|ABF93745.1| expressed kinase-like protein [Oryza sativa (japonica cultivar-group)] 208 506 PHE0010613_22404 7 Corn high oil DAG  1.00E−165 80 115450433 gb|ABF93745.1| expressed kinase-like protein [Oryza sativa (japonica cultivar-group)] 209 507 PHE0002720_22558 18 Corn DNA J protein 0 83 115463255 gb|AAV43840.1| putative DnaJ protein [Oryza sativa (japonica cultivar-group)] 210 508 PHE0011760_24005 31 Arabidopsis YODA 0 83 15222512 ref|NP_176557.1| YDA (YODA); protein kinase/ protein serine/threonine kinase/protein-tyrosine kinase [Arabidopsis thaliana] 211 509 PHE0010612_22397 3 Corn high oil nucleic  1.00E−165 77 115450431 gb|ABF93744.1| D111/G-patch acid binding domain-containing protein [Oryza sativa (japonica cultivar-group)] 211 509 PHE0010612_22403 7 Corn high oil nucleic  1.00E−165 77 115450431 gb|ABF93744.1| D111/G-patch acid binding domain-containing protein [Oryza sativa (japonica cultivar-group)] 212 510 PHE0010615_22400 3 Corn high oil 1.00E−32 28 125581548 gb|EAZ22479.1| hypothetical unknown protein protein OsJ_005962 [Oryza sativa (japonica cultivar-group)] 213 511 PHE0007411_17654 3 Rice putative 0 97 57899656 dbj|BAD87325.1| putative tafazzin isoform tafazzin isoform [Oryza sativa (japonica cultivar-group)] 214 512 PHE0010617_22402 3 Corn high oil 5.00E−98 69 115447203 dbj|BAD20134.1| hydrolase-like isochorismatase hydrolase-like protein protein [Oryza sativa (japonica cultivar-group)] 215 513 PHE0010610_22395 3 Corn high oil RING- 9.00E−27 75 2894379 emb|CAA74911.1| ring finger finger protein protein [Hordeum vulgare subsp. vulgare] 216 514 PHE0006883_16702 7 Corn glucosyl 0 93 136757 sp|P04713| Granule-bound transferase starch synthase 1, (GBSS-I) emb|CAA27574.1| glucosyl transferase [Zea mays] 217 515 PHE0010636_22408 3 Corn glucose 6- 0 89 2997589 gb|AAC08524.1| glucose-6- phosphate phosphate/phosphate- translocator translocator precursor [Zea mays] 217 515 PHE0010636_22410 7 Corn glucose 6- 0 89 2997589 gb|AAC08524.1|glucose-6- phosphate phosphate/phosphate- translocator translocator precursor [Zea mays] 218 516 PHE0011082_23038 30 Soy SAG13 like 3.00E−98 66 15239327 gb|AAO22710.1| putative short chain alcohol dehydrogenase [Arabidopsis thaliana] 219 517 PHE0009475_20462 15 Arabidopsis 0 100 15235072 ref|NP_194272.1| gibberellin gibberellin 20- 20-oxidase/gibberellin 3-beta- oxidase dioxygenase [Arabidopsis thaliana] 219 517 PHE0009475_20468 2 Arabidopsis 0 100 15235072 ref|NP_194272.1| gibberellin gibberellin 20- 20-oxidase/gibberellin 3-beta- oxidase dioxygenase [Arabidopsis thaliana] 219 517 PHE0009475_20899 1 Arabidopsis 0 100 15235072 ref|NP_194272.1| gibberellin gibberellin 20- 20-oxidase/gibberellin 3-beta- oxidase dioxygenase [Arabidopsis thaliana] 219 517 PHE0009475_21740 any Arabidopsis 0 100 15235072 ref|NP_194272.1| gibberellin gibberellin 20- 20-oxidase/gibberellin 3-beta- oxidasc dioxygenase [Arabidopsis thaliana] 219 517 PHE0009475_20469 30 Arabidopsis 0 100 15235072 ref|NP_194272.1| gibberellin gibberellin 20- 20-oxidase/gibberellin 3-beta- oxidase dioxygenase [Arabidopsis thaliana] 220 518 PHE0007415_17661 7 Corn EIL2 0 75 125543684 gb|EAY89823.1|hypothetical protein OsI_011056 [Oryza sativa (indica cultivar-group)] 221 519 PHE0006614_16129 22 Soy STN7-LHCII 0 72 15241093 emb|CAB82763.1| (1-4)-beta- protein kinase mannan endohydrolase-like protein [Arabidopsis thaliana] 222 520 PHE0010611_22396 3 Corn high oil flavin 0 77 116317828 gb|EAY92887.1| hypothetical containing protein OsI_014120 [Oryza monooxygenase sativa (indica cultivar-group)] 223 521 PHE0011719_23946 na Arabidopsis 1- 0 99 18410774 ref|NP_567052.1| 1- acylglycerol-3- acylglycerol-3-phosphate O- phosphate O- acyltransferase [Arabidopsis acyltransferase thaliana] 224 522 PHE0006861_16463 29 Arabidopsis 0 87 5734789 gb|AAD50054.1| Hypothetical unknown protein protein [Arabidopsis thaliana] 225 523 PHE0006568_16005 13 Corn receptor-like 0 60 115472561 dbj|BAC84489.1| putative protein kinase serine/threonine-specific protein kinase [Oryza sativa (japonica cultivar-group)] 226 524 PHE0010652_22429 3 Corn high oil tRNA  1.00E−172 94 115469828 dbj|BAD53799.1| putative FtsJ methyltransferase homolog 1 isoform b [Oryza sativa (japonica cultivar- group)] 227 525 PHE0008158_18448 7 ZMEN1 7.00E−65 56 115437056 dbj|BAD73580.1| zinc-binding protein-like [Oryza sativa (japonica cultivar-group)] 228 526 PHE0003316_20755 30 E. coli beta-glucuronidase 0 100 475169 emb|CAA83649.1| beta- with intron 2 from potato glucuronidase [synthetic light-inducible tissue-specific gene construct] 229 527 PHE0009478_20470 2 Corn gibberellin 20  1.00E−167 82 37359180 gb|AAN73384.1| putative oxidase gibberellin 20 oxidase [Oryza rufipogon] 229 527 PHE0009478_20900 1 Corn gibberellin 20  1.00E−167 82 37359180 gb|AAN73384.1| putative oxidase gibberellin 20 oxidase [Oryza rufipogon] 229 527 PHE0009478_20471 any Corn gibberellin 20  1.00E−167 82 37359180 gb|AAN73384.1| putative oxidase gibberellin 20 oxidase [Oryza rufipogon] 230 528 PHE0010395_21760 30 Soy DUF716 3.00E−84 55 124365521 gb|ABN09755.1| Proteinase inhibitor I4, serpin [Medicago truncatula] 231 529 PHE0010391_21753 30 Soy Unknown 7.00E−64 91 115463333 gb|AAV43818.1| unknown protein protein [Oryza sativa (japonica cultivar-group)] 232 530 PHE0010396_21761 30 Soy DUF716 2.00E−83 56 124365521 gb|ABN09755.1|Proteinase inhibitor I4, serpin [Medicago truncatula] 233 531 PHE0009511_22422 26 Cucurbita S-  1.00E−147 73 21239731 gb|AAM44307.1| S- adenosylmethionine adenosylmethionine decarboxylase decarboxylase [Citrofortunella mitis] 234 532 PHE0010614_22399 3 Corn high oil SOUL- 2.00E−94 80 115435220 dbj|BAA96146.1| putative like protein heme binding protein 2 [Oryza sativa (japonica cultivar-group)] 235 533 PHE0011420_23634 3 Corn unknown 0 91 115464535 ref|NP_001055867.1|Os05g0482600 protein [Oryza sativa (japonica cultivar-group)] 236 534 PHE0011454_23667 13 Corn H2B2 3.00E−36 87 122044864 sp|P05621| Wheat histone H2B.2 237 535 PHE0011443_24001 13 Corn H2B1 2.00E−39 77 1708107 sp|P54348| Maize histone H2B.5 (H2B) 238 536 PHE0011452_23665 13 Corn H3-2 3.00E−69 99 15232146 sp|P69246| Maize hHistone H3.2 239 537 PHE0010394_21758 30 Soy Sin3 associated 2.00E−52 82 115443887 dbj|BAD07609.1| putative P18 ploypeptide [Oryza sativa (japonica cultivar-group)] 240 538 PHE0010397_21762 30 Soy unknown 7.00E−17 57 82568700 dbj|BAE48663.1|Pm52 [Prunus protein mume] 241 539 PHE0010398_21763 30 Soy unknown 1.00E−17 56 82568700 dbj|BAE48663.1|Pm52 [Prunus protein mume] 242 540 PHE0010100_21467 20 Klebsiella nitrite 0 90 585562 gb|AAA25099.1| nitrite reductase reductase [Klebsiella oxytoca] 243 541 PHE0011503_23734 1 Corn ethylene 0 91 38607373 gb|AAR25566.1| ethylene receptor etr1 mutant receptor [Zea mays] 243 541 PHE0011503_23736 15 Corn ethylene 0 91 38607373 gb|AAR25566.1| ethylene receptor etr1 mutant receptor [Zea mays] 244 542 PHE0010099_21319 13 Klebsiella nitrate 0 87 18314343 gb|AAA25100.2| nitrate reductase large reductase large subunit subunit [Klebsiella oxytoca] 244 542 PHE0010099_21461 9 Klebsiella nitrate 0 87 18314343 gb|AAA25100.2| nitrate reductase large reductase large subunit subunit [Klebsiella oxytoca] 244 542 PHE0010099_21466 20 Klebsiella nitrate 0 87 18314343 gb|AAA25100.2| nitrate reductase large reductase large subunit subunit [Klebsiella oxytoca] 245 543 PHE0011269_23400 13 Arabidopsis 0 96 42562138 gb|AAF97271.1| meristem L1 HIO2019A layer homeobox protein like (ATML1) from Arabidopsis thaliana gb|U37589 and contains Transposase PF|01527, Homeobox PF|00046, and START PF|01852 domains. 246 544 PHE0008393_18762 20 Corn roothairless 1 0 95 34733383 gb|AAQ81632.1| roothairless 1 [Zea mays] 247 545 PHE0010223_21491 3 Corn sucrose 0 87 49066602 gb|AAT51689.1| sucrose transport protein 4 transport protein [Zea mays] 248 546 PHE0011613_23858 3 Corn WRI1  1.00E−109 56 85815798 dbj|BAE78578.1|aintegumenta- like [Oryza sativa (japonica cultivar-group)] 248 546 PHE0011613_23860 7 Corn WRI1  1.00E−109 56 85815798 dbj|BAE78578.1|aintegumenta- like protein [Oryza sativa (japonica cultivar-group)] 249 547 PHE0001582_22064 1 Corn ethylene 0 93 10241927 gb|AAR25568.1| ethylene receptor ETR1 like receptor [Zea mays] 250 548 PHE0007444_22314 18 Corn aminopropyl 0 94 74481421 gb|AAW57523.1| spermidine transferase synthase [Zea mays] 251 549 PHE0010543_22298 16 Corn en-like protein 4.00E−92 94 115498267 gb|ABI98712.1| terminal flower FDR2 1 [Zea mays] 252 550 PHE0010543_22323 12 Cen-like protein 3.00E−83 94 115498267 gb|ABI98712.1| terminal flower FDR2 1 [Zea mays] 253 551 PHE0011081_23033 30 Arabidopsis SUC2 0 88 15239921 ref|NP_199174.1|carbohydrate/ sugar transporter [Arabidopsis thaliana] 254 552 PHE0011075_23026 30 Wheat P-II 3.00E−62 77 125550734 gb|EAY96443.1| hypothetical protein OsI_017676 [Oryza sativa (indica cultivar-group)] 255 553 PHE0010100_21462 9 Klebsiella Nitrite 0 90 585562 sp|Q06458| Nitrite reductase reductase [NAD(P)H] large subunit [Klebsiella oxytoca] 256 554 PHE0009640_21775 30 Arabidopsis 3.00E−53 100 15236188 ref|NP_195203.1| unknown ME10609 protein [Arabidopsis thaliana] 257 555 PHE0010092_21307 13 Corn translation  1.00E−158 84 115452457 gb|ABF95443.1| Eukaryotic initiation factor 2 translation initiation factor 2 alpha subunit alpha subunit [Oryza sativa (japonica cultivar-group)] 258 556 PHE0004611_24123 13 Arabidopsis putative 0 89 12325237 gb|AAG52567.1| putative peptide transporter peptide transporter [Arabidopsis thaliana] 259 557 PHE0010093_21308 13 Corn translation  1.00E−162 85 115452457 gb|ABF95443.1| Eukaryotic initiation factor 2 translation initiation factor 2 alpha subunit alpha subunit [Oryza sativa (japonica cultivar-group)] 260 558 PHE0008605_23084 13 Arabidopsis putative 4.00E−40 98 15226943 gb|AAM62619.1| putative histone H2B histone H2B [Arabidopsis thaliana] 261 559 PHE0009939_21100 16 Arabidopsis glycine 0 98 15234036 ref|NP_195027.1| glycine dehydrogenase dehydrogenase [Arabidopsis thaliana] 262 560 PHE0009941_21105 8 Corn Moc1-like  1.00E−124 80 125540188 gb|EAY86583.1| hypothetical protein OsI_007816 [Oryza sativa (indica cultivar-group)] 263 561 PHE0009951_21135 8 Yeast QSR1-like  1.00E−115 93 6323104 sp|P41805| Yeast 60S ribosomal protein L10 (L9) (Ubiquinol-cytochrome C reductase complex subunit VI- requiring protein) 264 562 PHE0009943_21127 8 Arabidopsis QSR1-  1.00E−127 100 18408550 gb|AAM64974.1| 60S like ribosomal protein L10 [Arabidopsis thaliana] 265 563 PHE0009948_21132 8 Soy QSR1-like  1.00E−120 93 92870109 gb|ABE79479.1 |Ribosomal protein L10E [Medicago truncatula] 266 564 PHE0011084_23040 30 Soy 0 77 92896730 gb|ABE93328.1|Peptidase SNG1_sinapoylglu- S10, serine carboxypeptidase cose:malate [Medicago truncatula] sinapoyltransferase 267 565 PHE0008233_23042 30 Soy Phi-1 protein  1.00E−122 71 3759184 dbj|BAA33810.1| phi-1 [Nicotiana tabacum] 268 566 PHE0010854_22730 13 Soy regulator of G-  1.00E−160 58 22331342 ref|NP_189238.2| Regulator of protein signaling G-protein signaling 1 [Arabidopsis thaliana] 269 567 PHE0003797_23051 10 Corn DNA-binding 1.00E−44 63 1061306 emb|CAA56287.1| Dof2 [Zea protein Dof2 mays] 270 568 PHE0010194_21769 30 Arabidopsis putative 0 94 15235301 emb|CAB80722.1| putative endo-1,4-beta endo-1,4-beta glucanase glucanase [Arabidopsis thaliana] 271 569 PHE0010197_21429 13 Corn putative DNA 2.00E−25 72 115451027 gb|ABF94221.1| bHLH family binding protein protein [Oryza sativa (japonica cultivar-group)] 271 569 PHE0010197_21454 5 Corn putative DNA 2.00E−25 72 115451027 gb|ABF94221.1| bHLH family binding protein protein [Oryza sativa (japonica cultivar-group)] 271 569 PHE0010197_21455 16 Corn putative DNA 2.00E−25 72 115451027 gb|ABF94221.1| bHLH family binding protein protein[Oryza sativa (japonica cultivar-group)] 271 569 PHE0010197_21456 20 Corn putative DNA 2.00E−25 72 115451027 gb|ABF94221.1| bHLH family binding protein protein[Oryza sativa (japonica cultivar-group)] 271 569 PHE0010197_21770 30 Corn putative DNA 2.00E−25 72 115451027 gb|ABF94221.1| bHLH family binding protein protein [Oryza sativa (japonica cultivar-group)] 272 570 PHE0011665_23899 30 Arabidopsis  1.00E−146 96 15225630 gb|AAM20369.1| putative chlorophyll a/b chlorophyll a/b binding protein binding protein [Arabidopsis thaliana] 273 571 PHE0012178_24443 3 Corn putative chain 4.00E−99 78 115444353 dbj|BAD28032.1| putative C, structure of the chain C, structure of the plant plant transcriptional transcriptional regulator Pbf-2 regulator Pbf-2 [Oryza sativa (japonica cultivar-group)] 274 572 PHE0012170_24424 3 Arabidopsis 7.00E−40 74 30689607 gb|ABC96792.1| ARGOS-like AGROS-like [Arabidopsis thaliana] 275 573 PHE0011064_22994 4 Corn LPA1 0 85 115436512 dbj|BAD52962.1| unknown protein [Oryza sativa (japonica cultivar-group)] 275 573 PHE0011064_23000 8 Corn LPA1 0 85 115436512 dbj|BAD52962.1| unknown protein [Oryza sativa (japonica cultivar-group)] 275 573 PHE0011064_23002 18 Corn LPA1 0 85 115436512 dbj|BAD52962.1| unknown protein [Oryza sativa (japonica cultivar-group)] 275 573 PHE0011064_23003 9 Corn LPA1 0 85 115436512 dbj|BAD52962.1| unknown protein [Oryza sativa (japonica cultivar-group)] 275 573 PHE0011064_23004 10 Corn LPA1 0 85 115436512 dbj|BAD52962.1| unknown protein [Oryza sativa (japonica cultivar-group)] 276 574 PHE0010201_21768 30 Soy DNA-binding 9.00E−30 75 30689711 ref|NP_849712.1 | transcription protein regulator [Arabidopsis thaliana] 277 575 PHE0010838_22702 30 Soy PIN1 3.00E−32 71 25140423 gb|AAN71616.1| PIN-like protein [Gossypium hirsutum] 278 576 PHE0010201_21433 13 Soy DNA-binding 1.00E−29 75 30689711 ref|NP_849712.1| transcription protein regulator [Arabidopsis thaliana] 279 577 PHE0011446_23659 13 Corn histone H3-1 7.00E−59 87 166384 gb|AAA32655.1| histone H3 (H3-1.1) 280 578 PHE0001424_22077 9 Corn seed storage 1.00E−68 41 57233444 gb|AAW48295.1| pore-forming protein, 35K isoform toxin-like protein Hfr-2 AmA1 - [Triticum aestivum] 281 579 PHE0011445_23658 13 Corn putative 3.00E−71 89 115447529 dbj|BAD25356.1| putative elicitor-responsive elicitor-responsive gene-3 gene-3 [Oryza sativa (japonica cultivar-group)] 282 580 PHE0010090_21297 21 Corn receptor 0 79 115451705 gb|ABF94768.1| Receptor protein kinase protein kinase CLAVATA1 CLAVATA1 precursor, [Oryza sativa (japonica cultivar-group)] 283 581 PHE0012180_24445 7 Corn regulatory 0 83 138603 sp|P26307| Maize regulatory protein viviparous-1 protein viviparous-1 284 582 PHE0011083_23039 30 Soy SAG13 like 8.00E−87 63 15239327 ref|NP_196225.1|oxidoreductase; homolog dbj|BAA98195.1| short chain alcohol dehydrogenase- like [Arabidopsis thaliana] 285 583 PHE0011085_23041 30 Soy  1.00E−157 62 92896727 gb|ABE93325.1|Peptidase SNG1_sinapoylglu- S10, serine carboxypeptidase cose:malate [Medicago truncatula] sinapoyltransferase 286 584 PHE0012175_24440 3 Corn TSO1_like 0 62 115489476 gb|ABA99828.1| Tesmin/TSO1-like CXC domain containing protein [Oryza sativa (japonica cultivar-group)] 286 584 PHE0012175_24448 7 Corn TSO1_like 0 62 115489476 gb|ABA99828.1| Tesmin/TSO1-like CXC domain containing protein [Oryza sativa (japonica cultivar-group)] 287 585 PHE0012177_24442 3 Corn P24_like  1.00E−101 74 119638471 gb|ABL85062.1| expressed protein [Brachypodium sylvaticum] 288 586 PHE0011447_23660 13 Corn P0031D02.12 1.00E−71 80 115440763 gb|EAY76322.1| hypothetical protein protein OsI_004169 [Oryza sativa (indica cultivar-group)] 289 587 PHE0010194_21426 13 Arabidopsis putative 0 95 15235301 emb|CAB80722.1| putative endo-1,4-beta endo-1,4-beta glucanase glucanase [Arabidopsis thaliana] 290 588 PHE0011666_23900 30 Soy SPDS  1.00E−165 87 99083515 gb|ABF66657.1| spermidine synthase [Ammopiptanthus mongolicus] 291 589 PHE0011448_24160 13 Corn histone H4-2 2.00E−30 80 115479301 ref|NP_001063244.1| Os09g0433500 [Oryza sativa (japonica cultivar-group)] 292 590 PHE0008324_18636 13 Arabidopsis T27I1.4 0 86 15218372 ref|NP_172473.1| unknown protein protein [Arabidopsis thaliana] 293 591 PHE0006971_16875 13 Ceres82Rice  1.00E−124 84 125583584 gb|EAZ24515.1| hypothetical unknown protein protein OsJ_007998 [Oryza sativa (japonica cultivar-group)] 294 592 PHE0009939_21147 20 Arabidopsis glycine 0 98 15234036 ref|NP_195027.1| glycine dehydrogenase dehydrogenase [Arabidopsis thaliana] 295 593 PHE0009953_21137 9 Corn dicarboxylate 0 89 40363459 dbj|BAD06219.1| plastidic 2- translocator 1 oxoglutarate/malate transporter [Zea mays] 296 594 PHE0006907_16797 13 Corn 5.00E−94 60 115458524 ref|NP_001052862.1| DUF150_MON_ZM4 Os04g0438300 [Oryza sativa 1251 (japonica cultivar-group)] 297 595 PHE0008557_18970 13 Corn FAD_binding_6[1]::NAD_binding_1[1] 0 89 115455751 dbj|BAA07479.1| root ferredoxin-NADP reductase ferredoxin-NADP+ reductase [Oryza sativa (japonica cultivar-group)] 298 596 PHE0006443_15955 13 Arabidopsis putative 0 98 15226918 gb|AAL32813.1| putative SET- SET-domain protein domain protein [Arabidopsis thaliana] Selection Methods for Transgenic Plants with Enhanced Agronomic Trait

Within a population of transgenic plants regenerated from plant cells transformed with the recombinant DNA many plants that survive to fertile transgenic plants that produce seeds and progeny plants will not exhibit an enhanced agronomic trait. Selection from the population is necessary to identify one or more transgenic plant cells that can provide plants with the enhanced trait. Transgenic plants having enhanced traits are selected from populations of plants regenerated or derived from plant cells transformed as described herein by evaluating the plants in a variety of assays to detect an enhanced trait, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. These assays also may take many forms including, but not limited to, direct screening for the trait in a greenhouse or field trial or by screening for a surrogate trait. Such analyses can be directed to detecting changes in the chemical composition, biomass, physiological properties, morphology of the plant. Changes in chemical compositions such as nutritional composition of grain can be detected by analysis of the seed composition and content of protein, free amino acids, oil, free fatty acids, starch or tocopherols. Changes in biomass characteristics can be made on greenhouse or field grown plants and can include plant height, stem diameter, root and shoot dry weights; and, for corn plants, ear length and diameter. Changes in physiological properties can be identified by evaluating responses to stress conditions, for example assays using imposed stress conditions such as water deficit, nitrogen deficiency, cold growing conditions, pathogen or insect attack or light deficiency, or increased plant density. Changes in morphology can be measured by visual observation of tendency of a transformed plant with an enhanced agronomic trait to also appear to be a normal plant as compared to changes toward bushy, taller, thicker, narrower leaves, striped leaves, knotted trait, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other selection properties include days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance. In addition, phenotypic characteristics of harvested grain may be evaluated, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality. Although the plant cells and methods of this invention can be applied to any plant cell, plant, seed or pollen, e.g. any fruit, vegetable, grass, tree or ornamental plant, the various aspects of the invention are preferably applied to corn, soybean, cotton, canola, alfalfa, wheat and rice plants.

The following examples are included to demonstrate aspects of the invention, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific aspects which are disclosed and still obtain a like or similar results without departing from the spirit and scope of the invention.

Example 1. Plant Expression Constructs

This example illustrates the construction of plasmids for transferring recombinant DNA into plant cells which can be regenerated into transgenic plants of this invention

A. Plant Expression Constructs for Corn Transformation

A base corn transformation vector pMON93039, as set forth in SEQ ID NO: 30521, illustrated in Table 3 and FIG. 2, was fabricated for use in preparing recombinant DNA for Agrobacterium-mediated transformation into corn tissue.

TABLE 3 Coordinates of Function Name Annotation SEQ ID NO: 30521 Agrobacterium B-AGRtu.right border Agro right border sequence, 11364-11720 T-DNA transfer essential for transfer of T-DNA. Gene of interest E-Os.Act1 Upstream promoter region of the  19-775 expression rice actin 1 gene cassette E-CaMV.35S.2xA1- Duplicated 35S A1-B3 domain  788-1120 B3 without TATA box P-Os.Act1 Promoter region of the rice actin 1 1125-1204 gene L-Ta.Lhcb1 5′ untranslated leader of wheat 1210-1270 major chlorophyll a/b binding protein I-Os.Act1 First intron and flanking UTR exon 1287-1766 sequences from the rice actin 1 gene T-St.Pis4 3′ non-translated region of the 1838-2780 potato proteinase inhibitor II gene which functions to direct polyadenylation of the mRNA Plant selectable P-Os.Act1 Promoter from the rice actin 1 gene 2830-3670 marker L-Os.Act1 First exon of the rice actin 1 gene 3671-3750 expression I-Os.Act1 First intron and flanking UTR exon 3751-4228 cassette sequences from the rice actin 1 gene TS-At.ShkG-CTP2 Transit peptide region of 4238-4465 Arabidopsis EPSPS CR-AGRtu.aroA- Coding region for bacterial strain 4466-5833 CP4.nat CP4 native aroA gene. T-AGRtu.nos A 3′ non-translated region of the 5849-6101 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Agrobacterium B-AGRtu.left border Agro left border sequence, essential 6168-6609 T-DNA transfer for transfer of T-DNA. Maintenance in OR-Ec.oriV-RK2 The vegetative origin of replication 6696-7092 E. coli from plasmid RK2. CR-Ec.rop Coding region for repressor of 8601-8792 primer from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of replication 9220-9808 from the E. coli plasmid ColE1. P-Ec.aadA-SPC/STR Promoter for Tn7 10339-10380 adenylyltransferase (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 10381-11169 SPC/STR adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 11170-11227 adenylyltransferase (AAD(3″)) gene of E. coli.

Other base vectors similar to the one described above were also constructed as listed in Table 4. These base corn transformation vectors are also used for wheat and rice transformations. See Table 4 for a summary of base vectors and base vector ID's which are referenced in Table 2. Also see Table 5 for a summary of regulatory elements used in the gene expression cassettes for these base vectors and the SEQ ID NOs for these elements.

Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base vectors as referenced in Table 2.

TABLE 4 Base Vector ID Corn Base Vector 1 pMON92709 2 pMON92713 3 pMON92715 4 pMON92716 5 pMON92718 6 pMON92719 7 pMON92721 8 pMON92722 9 pMON92724 10 pMON92729 11 pMON93025 12 pMON93026 13 pMON93039 14 pMON93043 15 pMON94781 16 pMON94830 17 pMON99009 18 pMON99048 19 pMON99051 20 pMON99052 21 pMON100406 Soy And Canola Base Vector 22 pMON74537 23 pMON74552 24 pMON74553 25 pMON82053 26 pMON83145 27 pMON92671 28 pMON97027 29 pMON99006 30 pMON100407 31 pMON102815 32 pMON102819 Cotton Base Vector 33 pMON95549 34 pMON99053

TABLE 5 SEQ SEQ SEQ Base vector Promoter ID NO Leader ID NO Intron ID NO pMON92709 P-Os.GT1 30469 L-Os.GT1 30493 I-Zm.DnaK 30516 pMON92713 P-Zm.P39486 30470 L-Zm.39486 30494 I-Zm.DnaK 30516 pMON92715 P-Hv.Per1 30471 L-Hv.Per1 30495 I-Zm.DnaK 30516 pMON92716 P-Zm.FDA 30472 L-Zm.FDA 30496 I-Zm.DnaK 30516 pMON92718 P-Zm.CLK1 30473 L-Zm.Cik1 30497 I-Zm.Cik1 30517 pMON92719 P-Zm.RAB17 30474 L-Zm.RAB17 30498 I-Zm.DnaK 30516 pMON92721 P-Zm.SzeinC1 30475 L-Zm.SzeinC1 30499 I-Zm.DnaK 30516 pMON92722 P-CaMV.35S-enh 30476 L-CaMV.35S 30500 I-Zm.DnaK 30516 pMON92724 P-Zm.- 30477 L-Zm.PPDK 30501 I-Zm.DnaK 30516 636aldolase-0:1:2 + P-Zm.PPDK pMON92729 P-Zm.PPDK 30478 L-Zm.PPDK 30501 I-Zm.DnaK 30516 pMON93025 P-At.SUC2 30479 L-At.SUC2 30502 I-Zm.DnaK 30516 pMON93026 P-Os.H1 30480 L-Os.H1 30503 I Zm.DnaK 30516 pMON93039 E-Os.Act1 + E- 30481 L-Ta.Lhcb1 30504 I-Os.Act1 30518 CaMV.35S.2xA1- B3 + P-Os.Act1 pMON93043 P-Zm.EM 30482 L-Zm.EM 30505 I-Zm.DnaK 30516 pMON94781 P-Zm.Brittle-2 30483 L-Zm.Brittle-2 30506 I-Zm.DnaK 30516 pMON94830 P-Os.Act16 30484 L-Os.Act16 30507 I-Os.Act16 30519 pMON99009 P-CaMV.35S-enh 30476 L-Ph.DnaK 30508 None / pMON99048 P-Os.Act1 + E- 30485 L-Ta.Lhcb1 30504 I-Os.Act1 30518 CaMV.35S.2xA1- B3 pMON99051 P-Zm.Kn1 30486 L-Zm.Kn1 30509 None / pMON99052 P-Os.Rcc.3 30487 L-Os.Rcc3 30510 I-Zm.DnaK 30516 pMON100406 P-Zm.Kn1 30486 L-Zm.Kn1 30509 I-Zm.DnaK 30516 pMON74537 P-At.RbcS4 30488 L-At.RbcS4 30511 None / pMON74552 P-CaMV.35S-enh 30476 None / None / pMON74553 P-CaMV.35S-enh 30476 None / None / pMON82053 P-CaMV.35S-enh 30476 None / None / pMON83145 P-Gm.Hsp20 30489 L-Gm.Hsp20 30512 None / pMON92671 P-At.SAMS3 30490 L-At.SAMS3 30513 I-At.SAMS3 30520 pMON97027 P-At.GRP7 30491 L-At.GRP7 30514 None / pMON99006 P-CaMV.35S-enh 30476 None / None / pMON100407 P-CaMV.35S-enh 30476 L-Ph.DnaK 30508 None / pMON102815 P-At.Erecta 30492 L-At.Erecta 30515 None / pMON102819 P-CaMV.35S-enh 30476 None / None / pMON95549 P-At.SAMS3 30490 L-At.SAMS3 30513 I-At.SMAS3 30520 pMON99053 P-CaMV.35S-enh 30476 L-Ph.DnaK 30508 None / For construct pMON94830, the L-Os.Act16 leader sequence (SEQ ID IN 30507) is interrupted by the I-Os.Act16 intron sequence (SEQ ID NO 30519) between nucleotide positions 3344 and 3861.

B. Plant Expression Constructs for Soy and Canola Transformation

Vectors for use in transformation of soybean and canola were also prepared. Elements of an exemplary common expression vector pMON82053 are shown in Table 6 below and FIG. 3. Another example of elements used in plant expression cassette for gene of interest such as PEP SEQ ID NOs 366 and 521 were the P-Gm.Sphas1 promoter (SEQ ID NO: 30524) and the L-Gm.Sphas1 leader (SEQ ID NO: 30525) sequences.

TABLE 6 Coordinates of Function Name Annotation SEQ ID NO: 30522 Agrobacterium T- B-AGRtu.left border Agro left border sequence, essential for 6144-6585 DNA transfer transfer of T-DNA. Plant selectable P-At.Act7 Promoter from the Arabidopsis actin 7 gene 6624-7861 marker expression L-At.Act7 5′UTR of Arabidopsis Act7 gene cassette I-At.Act7 Intron from the Arabidopsis actin7 gene TS-At.ShkG-CTP2 Transit peptide region of Arabidopsis 7864-8091 EPSPS CR-AGRtu.aroA- Synthetic CP4 coding region with dicot 8092-9459 CP4.nno_At preferred codon usage. T-AGRtu.nos A 3′ non-translated region of the nopaline 9466-9718 synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Gene of interest P-CaMV.35S-enh Promoter for 35S RNA from CaMV  1-613 expression cassette containing a duplication of the −90 to −350 region. T-Gb.E6-3b 3′ untranslated region from the fiber protein  688-1002 E6 gene of sea-island cotton. Agrobacterium T- B-AGRtu.right Agro right border sequence, essential for 1033-1389 DNA transfer border transfer of T-DNA. Maintenance in E. coli OR-Ec.oriV-RK2 The vegetative origin of replication from 5661-6057 plasmid RK2. CR-Ec.rop Coding region for repressor of primer from 3961-4152 the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of replication from the 2945-3533 E. coli plasmid ColE1. P-Ec.aadA-SPC/STR Promoter for Tn7 adenylyltransferase 2373-2414 (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 adenylyltransferase 1584-2372 SPC/STR (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 adenylyltransferase 1526-1583 (AAD(3″)) gene of E. coli.

Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base vectors as referenced in Table 2.

C. Cotton Transformation Vector

Plasmids for use in transformation of cotton were also prepared. Elements of an exemplary common expression vector pMON99053 are shown in Table 7 below and FIG. 4. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base vectors as referenced in Table 2.

TABLE 7 Coordinates of SEQ ID NO: Function Name Annotation 30523 Agrobacterium B-AGRtu.right border Agro right border sequence,  1-357 T-DNA transfer essential for transfer of T- DNA. Gene of interest Exp-CaMV.35S-enh + Ph.DnaK Enhanced version of the 35S  388-1091 expression RNA promoter from CaMV cassette plus the petunia hsp70 5′ untranslated region T-Ps.RbcS2-E9 The 3′ non-translated region of 1165 1797 the pea RbcS2 gene which functions to direct polyadenylation of the mRNA. Plant selectable Exp-CaMV.35S Promoter and 5′ untranslated 1828-2151 marker region from the 35S RNA of expression CaMV cassette CR-Ec.nptII-Tn5 Coding region for neomycin 2185-2979 phosphotransferase gene from transposon Tn5 which confers resistance to neomycin and kanamycin. T-AGRtu.nos A 3′ non-translated region of 3011-3263 the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Agrobacterium B-AGRtu.left border Agro left border sequence, 3309-3750 T-DNA transfer essential for transfer of T- DNA. Maintenance in OR-Ec.oriV-RK2 The vegetative origin of 3837-4233 E. coli replication from plasmid RK2. CR-Ec.rop Coding region for repressor of 5742-5933 primer from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of 6361-6949 replication from the E. coli plasmid ColE1. P-Ec.aadA-SPC/STR Promoter for Tn7 7480-7521 adenylyltransferase (AAD(3″)) CR-Ec.aadA-SPC/STR Coding region for Tn7 7522-8310 adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 8311-8368 adenylyltransferase (AAD(3″)) gene of E. coli.

Example 2. Corn Transformation

This example illustrates plant cell transformation methods useful in producing transgenic corn plant cells, plants, seeds and pollen of this invention and the production and identification of transgenic corn plants and seed with an enhanced trait, i.e. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plasmid vectors were prepared by cloning DNA identified in Table 2 in the identified base vectors for use in corn transformation of corn plant cells to produce transgenic corn plants and progeny plants, seed and pollen.

For Agrobacterium-mediated transformation of corn embryo cells corn plants of a readily transformable line are grown in the greenhouse and ears are harvested when the embryos are 1.5 to 2.0 mm in length. Ears are surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Immature embryos are isolated from individual kernels on surface sterilized ears. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature. Immature maize embryo cells are inoculated with Agrobacterium shortly after excision, and incubated at room temperature with Agrobacterium for 5-20 minutes. Immature embryo plant cells are then co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark. Co-cultured embryos are transferred to selection media and cultured for approximately two weeks to allow embryogenic callus to develop. Embryogenic callus is transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals. Transformed plant cells are recovered 6 to 8 weeks after initiation of selection.

For Agrobacterium-mediated transformation of maize callus immature embryos are cultured for approximately 8-21 days after excision to allow callus to develop. Callus is then incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration. The callus and Agrobacterium are co-cultured without selection for 3-6 days followed by selection on paromomycin for approximately 6 weeks, with biweekly transfers to fresh media. Paromomycin resistant calli are identified about 6-8 weeks after initiation of selection.

For transformation by microprojectile bombardment maize immature embryos are isolated and cultured 3-4 days prior to bombardment. Prior to microprojectile bombardment, a suspension of gold particles is prepared onto which the desired recombinant DNA expression cassettes are precipitated. DNA is introduced into maize cells as described in U.S. Pat. Nos. 5,550,318 and 6,399,861 using the electric discharge particle acceleration gene delivery device. Following microprojectile bombardment, tissue is cultured in the dark at 27° C. Additional transformation methods and materials for making transgenic plants of this invention, for example, various media and recipient target cells, transformation of immature embryos and subsequence regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526 and U.S. patent application Ser. No. 09/757,089, which are incorporated herein by reference.

To regenerate transgenic corn plants a callus of transgenic plant cells resulting from transformation and selection is placed on media to initiate shoot development into plantlets which are transferred to potting soil for initial growth in a growth chamber at 26° C. followed by a mist bench before transplanting to 5 inch pots where plants are grown to maturity. The regenerated plants are self-fertilized and seed is harvested for use in one or more methods to select seeds, seedlings or progeny second generation transgenic plants (R2 plants) or hybrids, e.g. by selecting transgenic plants exhibiting an enhanced trait as compared to a control plant.

Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as reported in Example 7.

Example 3. Soybean Transformation

This example illustrates plant transformation useful in producing the transgenic soybean plants of this invention and the production and identification of transgenic seed for transgenic soybean having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

For Agrobacterium mediated transformation, soybean seeds are imbided overnight and the meristem explants excised. The explants are placed in a wounding vessel. Soybean explants and induced Agrobacterium cells from a strain containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette are mixed no later than 14 hours from the time of initiation of seed imbibition, and wounded using sonication. Following wounding, explants are placed in co-culture for 2-5 days at which point they are transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots. Resistant shoots are harvested approximately 6-8 weeks and placed into selective rooting media for 2-3 weeks. Shoots producing roots are transferred to the greenhouse and potted in soil. Shoots that remain healthy on selection, but do not produce roots are transferred to non-selective rooting media for an additional two weeks. Roots from any shoots that produce roots off selection are tested for expression of the plant selectable marker before they are transferred to the greenhouse and potted in soil. Additionally, a DNA construct can be transferred into the genome of a soybean cell by particle bombardment and the cell regenerated into a fertile soybean plant as described in U.S. Pat. No. 5,015,580, herein incorporated by reference.

Transgenic soybean plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as reported in Example 7.

Example 4. Cotton Transgenic Plants with Enhanced Agronomic Traits

Cotton transformation is performed as generally described in WO00036911 and in U.S. Pat. No. 5,846,797. Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 298 are obtained by transforming with recombinant DNA from each of the genes identified in Table 1. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, i.e. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, i.e. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, i.e. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.

The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.

Example 5. Canola Transformation

This example illustrates plant transformation useful in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Tissues from in vitro grown canola seedlings are prepared and inoculated with overnight-grown Agrobacterium cells containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterization are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant

Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as reported in Example 7.

Example 6. Homolog Identification

This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 2 which is used to provide transgenic seed and plants having enhanced agronomic traits. From the sequence of the homologs, homologous DNA sequence can be identified for preparing additional transgenic seeds and plants of this invention with enhanced agronomic traits.

An “All Protein Database” was constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a polynucleotide sequence provided herein was obtained, an “Organism Protein Database” was constructed of known protein sequences of the organism; it is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.

The All Protein Database was queried using amino acid sequences provided herein as SEQ ID NO: 299 through SEQ ID NO: 596 using NCBI “blastp” program with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list was kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes of the polynucleotides provided herein, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.

The Organism Protein Database was queried using polypeptide sequences provided herein as SEQ ID NO: 299 through SEQ ID NO: 596 using NCBI “blastp” program with E-value cutoff of 1e-4. Up to 1000 top hits were kept. A BLAST searchable database was constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of 1e-8. The hit with the best E-value was compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Homologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 597 through SEQ ID NO: 30468. These relationships of proteins of SEQ ID NO: 299 through 596 and homologs of SEQ ID NO: 597 through 30468 are identified in Table 8. The source organism for each homolog is found in the Sequence Listing.

TABLE 8 PEP SEQ ID NO: homolog SEQ ID NOs 299: 22505 17330 17332 3832 26661 24604 24601 26617 26553 26585 26591 26640 26582 26471 26635 26572 26576 26556 26609 26423 25650 26551 2373 2405 24690 25446 25450 26422 26473 25340 10489 21242 21238 21241 21279 24723 24725 25494 25690 25164 16529 7978 10037 16615 16621 11055 12923 6955 7874 7948 7839 8664 12144 14757 17096 14796 14828 26829 12171 21124 23048 20000 23191 22333 20933 15625 22212 19851 28192 27896 22998 22992 15629 28137 24133 22151 29931 985 2060 944 28955 28930 28990 29965 15658 21486 21255 20071 19073 19014 18158 18127 18109 15620 2239 2233 16398 14851 11657 12588 11744 14570 13748 13790 12143 12170 12173 12919 15622 15628 15656 15604 16393 16394 16392 12916 11037 22432 8701 24656 19135 19853 7817 18495 2869 8263 29437 29438 22440 22435 21711 22465 21146 17031 19010 21907 27742 22415 5429 1188 5421 18365 23435 12382 12090 12087 10571 18362 23640 15382 987 6445 6417 5413 8888 2538 24892 15423 1089 1127 5417 21701 24630 24633 21702 21705 25589 25558 21697 7438 22989 17339 1478 1506 1479 9199 25171 26307 1472 25424 25418 5394 23942 8884 8887 12914 23541 300: 16906 20559 21806 5055 4905 9056 13559 14510 4167 13364 13441 11165 3862 1913 6572 9353 29885 5672 23667 20433 11405 26215 8142 13983 9317 1831 16167 26355 11049 12454 607 20163 21550 8941 3691 19336 8960 11635 2500 12784 9832 13853 14431 6891 25892 24022 26873 8074 10050 6314 15883 23231 829 4758 4754 28646 4717 20464 9858 7971 12622 20501 4271 12195 9291 19503 21548 4124 10854 26029 12272 1775 25590 22837 22812 22556 10678 16223 25625 21334 8456 22176 14327 14302 17822 17624 16859 16850 17780 17619 17629 16852 10588 10650 1001 29219 15690 20293 25766 12151 21485 14320 17504 15478 15477 15066 15835 30365 30421 2696 20311 3417 19744 18488 3839 8782 17965 3743 3775 17509 17514 7091 6457 12394 12411 4075 4077 17590 21909 28286 3388 16788 15982 7848 29135 20349 19157 14248 29979 17396 17358 17398 17407 17324 17410 17366 17403 17357 17368 17360 19996 19846 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24565 16656 23229 26118 15206 19896 896 30168 26836 24841 24102 16849 16990 10451 11525 562 13157 14350 26264 3941 29121 18656 26496 29429 13386 6707 20627 12828 26769 638 20839 28624 18060 12109 21489 8385 8389 29785 3731 29847 20504 29916 11086 16445 24284 14179 24668 24107 24106 9456 4469 9743 26756 18494 14533 16275 1313 20351 23579 561 28151 27584 26925 20778 1598 14158 14079 24275 637 16709 564: 25129 27368 25249 29970 4685 4766 10275 29055 21313 10701 19680 9935 16488 8177 4015 27951 25825 21512 20368 27128 9690 12146 27413 15195 23828 11841 5189 14776 9064 21233 26231 12002 11133 9018 15501 26127 12008 11129 7116 16009 27954 10924 12108 21081 12026 22330 27916 24283 7140 27779 24073 4136 30112 11168 1115 22933 22672 19676 21195 1111 11985 28917 22696 16189 13287 3293 12420 30163 6141 3686 20573 16193 23458 4617 4625 24189 11578 9003 13450 11577 11574 12862 21165 16191 11772 16870 29589 7318 7287 7322 27518 12423 6771 29765 18959 18928 6767 18139 771 6718 10234 14176 7640 29596 7371 15272 14212 10238 5355 23723 23465 10565 7485 1227 22251 16546 24889 29958 25556 5655 8828 28823 28380 2635 12575 21856 6971 17870 15410 13234 11015 22504 8340 8342 9158 18685 29258 8072 29470 19267 18350 2117 14539 725 3730 13289 14559 10188 15006 7581 22282 5390 2261 10220 2021 22170 22174 22172 16620 6756 12246 18575 17265 21720 17791 3742 25238 7440 19956 1764 19482 23779 565: 13444 29969 14565 8761 4609 27488 15129 21484 10063 3692 15266 13584 9606 3133 29198 12289 29118 4198 3469 1246 9029 22236 566: 12946 14206 6593 6591 25758 19731 19754 23642 567: 13038 4724 16883 8660 7271 2574 7312 7307 19099 16463 22752 16786 24534 1935 18448 8772 9405 12044 16340 27473 568: 20417 27886 19619 7800 1272 3823 7082 27564 15616 24116 14223 27721 8014 22783 8325 24621 17123 20009 29665 28581 24641 24616 24828 13057 16913 9997 29744 10107 29748 29746 22723 14234 2110 8575 10591 9773 9777 8670 11915 18424 9511 18564 20764 13787 18423 11187 18604 3516 20154 14600 14603 19437 26638 27689 27696 27693 22261 12113 10921 9824 7009 7004 8973 8978 6447 1337 1352 16043 21920 21961 8161 8211 26300 13172 13843 20552 12458 14142 9797 19787 3606 25773 16317 23816 3673 899 13278 22264 22235 22260 22267 17224 14236 10840 11111 11109 11107 19732 3976 5933 6842 28949 20695 9231 2267 22271 9587 27307 19107 21070 15001 21236 14427 27038 20250 12766 12763 6036 12377 9763 12793 507 14396 569: 1581 16146 11925 5139 11665 14692 30172 570: 1205 1202 23043 18478 21335 24048 24042 12899 18378 18376 6551 9413 9412 19940 19978 19981 2128 18413 18415 16198 16668 3185 15855 9352 14616 2960 2967 2966 4462 25905 11227 28186 984 13539 20758 20789 20750 20753 20749 25229 28534 17690 22452 24103 19988 21788 25087 19912 21275 19982 19909 24881 24899 26679 18852 27639 12055 16381 1897 1894 1892 20060 7377 10185 12191 13610 6686 27612 27664 3919 27641 10110 28531 28470 2758 4227 10669 8133 24960 23679 11153 19321 30078 21051 17845 17557 1936 23577 27609 28429 27692 28464 27698 27667 28432 28424 27637 19872 26730 18303 18438 18412 10396 9203 29169 12043 1965 24374 25660 17724 16729 20884 2141 19907 22922 27089 2063 26239 19936 19119 21272 19915 19985 19916 18368 18306 18331 18333 18338 17515 18481 17665 16401 13021 427 23518 7850 571: 15818 24500 6249 24365 21416 9058 5044 3647 14963 14493 20694 7254 20765 572: 28807 27051 3150 20358 5777 13209 5111 9645 17113 16565 22552 16503 25832 29107 1460 14728 21817 17382 20312 10501 20673 3346 1922 10077 6744 26143 7881 8571 364 26287 15280 26997 9989 27429 4294 26013 754 22726 25117 573: 8315 18414 30224 15804 2638 19500 17309 12992 30378 9019 1704 6981 7658 9420 23401 574: 19688 10946 17787 18811 24157 19726 16146 16140 13361 26217 825 17239 11925 5139 1815 428 13932 5348 14692 376 9975 30172 569 19165 576 29573 575: 4786 9635 22533 22517 6361 6393 742 9918 3287 10618 13765 22118 15728 12502 26571 17426 25481 6770 9626 2081 11885 24724 2078 13738 28822 8819 576: 19688 10946 17787 18811 24157 19726 16146 16140 13361 26217 825 17239 11925 5139 1815 428 13932 5348 14692 376 9975 30172 569 19165 574 29573 577: 11584 13724 29524 9554 16616 11861 29446 29504 29601 2685 2666 2692 1388 2697 1585 14288 1255 23869 7127 24502 19874 27071 12831 23261 4734 874 23045 23769 7502 28061 18457 15556 15559 15561 15555 15529 21912 15390 8535 8958 22252 24498 13117 25178 30459 15583 4752 23038 18254 7244 10345 20327 23212 5007 30091 7554 22684 5719 606 15301 14483 792 29861 15027 18648 7016 13651 1770 16899 16855 28048 662 18404 15455 14827 22321 11701 24050 10538 15416 15419 15425 15460 15427 15380 15459 2809 13727 17094 9390 1327 6658 9556 6697 578: 11761 19089 16165 8711 2759 12674 13415 29879 7066 579: 22555 27884 11448 8273 27880 8275 11446 27878 27874 3478 15805 11443 23102 23280 14976 1219 13309 22763 580: 7938 7964 1841 14824 14760 24052 3138 28102 21222 21218 21226 13120 4265 5711 11048 27430 17350 25395 9698 14345 25391 19114 11354 25539 2802 28086 19052 1394 4583 3706 3705 5387 4585 14414 5998 1847 27344 16676 16678 22469 24958 7905 7870 3660 12098 9513 6150 581: 12041 23443 2888 28895 11471 11483 11474 21745 12751 8116 16160 16162 17998 4000 27970 9384 5381 3441 24737 859 26362 24708 6811 6754 18178 22419 15989 15143 14642 1282 27419 18937 18587 23984 7343 15826 15863 17425 1009 8802 9588 7086 17485 1240 10670 10668 20548 27277 9613 19477 15631 11051 11046 11023 10988 10990 11021 11017 10994 10992 11019 11052 11014 9124 29772 24903 30361 12677 12681 17414 12679 21760 22304 26366 7605 27534 6568 582: 19546 7100 21078 29472 26206 14606 8808 9347 21542 10893 23028 28069 9435 27011 4314 15686 20175 18297 20143 6089 6122 27189 27017 26037 25820 24689 6779 23568 2628 19337 27084 30085 8185 3032 16480 5557 2421 18364 24072 19813 12996 10951 13094 7636 15739 29267 10609 16613 16763 26659 2575 17702 15594 12665 29225 8278 9180 28016 29556 25090 24005 9907 28287 24942 24941 5491 2270 16971 5215 5054 5062 5059 16969 22674 10175 10170 10172 10072 29929 10173 20423 14928 14922 8299 8043 26409 7503 3588 26584 28658 1029 12685 28830 25587 9165 17300 30326 23962 7436 12369 23509 16214 8176 29489 18480 2148 4847 19133 516 24058 10954 800 11217 583: 25129 27368 25249 29970 4685 30235 4766 10275 29055 24740 20607 21313 10701 19680 16488 9935 4015 8177 27951 25825 21512 20368 27128 9690 4877 27413 15195 23828 20916 28202 14776 9064 21233 26231 20077 25077 12008 9018 15501 12108 12002 11133 16009 26127 12026 11129 28917 7116 30112 24073 16189 22672 22330 10924 27779 27954 1115 22933 1111 21195 27916 24283 21081 30163 11168 19676 11985 4136 22696 7140 13287 24189 3293 11578 16193 20573 23458 4617 4625 9003 3686 12420 6141 13450 11577 11574 12862 11772 16870 29589 7287 7318 7322 27518 12423 6771 29765 18959 771 6718 10234 29596 14176 7371 7640 14212 15272 23723 10238 23465 1227 22251 16546 24889 29958 28823 8828 5655 25556 28380 2635 12575 6971 15410 21856 22504 8340 18685 29258 9158 8072 29470 18350 19267 2117 14539 725 3730 14559 10188 13289 15006 7581 5390 22282 2261 10220 2021 22170 22172 22174 16620 13494 14407 21902 17265 6756 12246 18575 21720 17791 3742 25238 7440 19956 4913 1764 19482 23676 564 28187 21453 11680 584: 2555 25500 14030 22659 25613 8260 27377 29793 1177 23381 14036 15968 21609 6826 5584 2182 28639 5929 1090 9967 16653 19423 6909 27061 805 16595 11380 27033 585: 16495 15818 18613 27890 10799 11700 27624 27254 9740 5044 6485 14963 14493 4453 8639 8663 8638 8637 9491 30129 23337 20765 19015 16487 586: 7759 1528 23333 853 16894 13376 11592 18242 15920 8992 587: 20417 27886 19619 7800 1272 3823 7082 27564 15616 24116 14223 27721 8014 22783 8325 24621 17123 20009 29665 28581 24641 24616 24828 13057 16913 9997 29744 10107 29748 29746 22723 14234 2110 8575 10591 9773 9777 8670 11915 18424 9511 18564 20764 13787 18423 11187 18604 3516 20154 14600 14603 19437 26638 27689 27696 27693 22261 12113 10921 9824 7009 7004 8973 8978 6447 1337 1352 16043 21920 21961 8161 8211 26300 13172 13843 20552 12458 14142 9797 19787 3606 25773 16317 23816 3673 899 13278 22264 22235 22260 22267 17224 14236 10840 11111 11109 11107 19732 3976 5933 6842 28949 20695 9231 2267 22271 9587 27307 19107 21070 15001 21236 14427 27038 20250 12766 12763 6036 12377 27914 9763 12793 568 588: 26090 24906 7328 16079 13640 1998 3987 14369 10118 24547 10168 19534 14201 4351 29751 23972 19048 19518 16929 12836 10980 5385 12514 8603 21615 14006 9621 29755 3278 9131 13564 783 18177 14122 16367 23240 18197 10484 27976 27790 10726 28360 7845 8361 7541 3978 10445 26641 1937 8810 18305 17353 26604 14422 26491 13341 8502 7149 14121 22354 27631 850 24218 22409 8455 30360 24294 14091 30220 23301 12792 17439 5642 24682 2394 781 21304 19627 7391 21743 2420 8426 27392 19043 22515 29067 5266 5679 8170 6456 10383 8388 22771 8450 17154 17655 21229 10695 22850 20714 3703 27996 24666 29419 13898 25251 2927 968 25866 11823 11437 11556 29559 28036 22558 28576 18030 644 20487 13123 21755 11073 8138 4868 5476 24215 8521 23457 22084 29764 12464 14383 27005 11776 28824 9025 18016 15103 18931 28602 8158 17472 1453 1990 16594 2573 20483 22565 23359 4684 14747 21853 24807 9107 9108 22028 24031 21991 26569 29011 5830 3328 15099 15130 21719 26251 13720 2076 22740 19986 24231 21220 18601 2781 26295 4537 1807 15313 11247 9328 2456 2455 2459 13267 13269 451 450 9730 9757 9762 21426 14657 11571 10874 15508 22276 22496 21391 21149 21996 21999 14338 14342 14140 14341 14363 15131 6669 14372 14890 14882 14886 14908 30442 13868 10627 14633 10628 10603 9996 18761 17083 26475 9727 16415 22604 16765 21893 21349 22764 341 3311 21992 8269 28346 13382 24297 24316 13140 2970 22223 763 16890 3910 16235 11545 28077 2792 23797 2309 7723 10108 12589 10780 13561 10432 24018 30465 23985 23865 12964 15841 26552 12280 10917 589: 21641 11914 23866 8645 13613 9312 23237 9134 23388 20043 2701 16767 28224 13756 18982 19274 23559 11811 2974 2235 28082 19162 8555 18862 24954 8256 20898 18136 10706 4529 15333 26671 4930 16619 29659 25935 24554 12329 15453 22322 9282 7014 23385 24862 14339 14577 13104 29724 6660 590: 1370 1803 10479 6604 11379 22320 2150 19084 8835 21367 3715 27142 28468 16052 29977 20304 15104 17160 22606 11506 10642 20938 19470 5997 2431 12142 10998 8140 2012 692 591: 20634 29046 27023 27018 27020 15445 17319 8384 8435 8439 4475 26372 26378 20484 17008 16211 767 2381 11826 27301 16213 17011 3572 27818 17652 27668 7815 11633 10323 7206 6849 28423 21614 28759 10404 11171 1722 14717 6437 5521 13143 26232 22628 28738 15781 15775 15777 23480 13052 16215 17016 22902 27289 27188 24044 24290 592: 21053 5637 13367 30097 30098 1714 4293 13481 14355 1206 1181 7897 14745 9179 2803 2806 19460 10635 28838 25830 16687 19459 23427 9319 15848 15846 12390 12391 10033 21274 8353 18944 2176 14748 9271 11074 12439 7936 20697 13928 20737 15591 1381 1363 5045 5043 23810 15873 18769 26971 26972 9219 3214 3212 2831 2833 16064 6039 24993 24991 27439 27438 29207 1634 19383 24416 24418 16903 11802 13429 2494 28555 28557 4328 3269 3272 14997 1597 27111 25193 9655 13046 13048 6270 7198 27215 1146 26515 26517 21921 15283 27402 27868 9639 16209 8679 15709 27332 20494 13930 5116 6353 7756 7601 8986 9515 1362 1365 685 24332 25918 25928 20497 12076 973 974 7589 1314 2849 7200 21813 9155 9156 10841 19587 19589 6171 8235 16570 3531 3526 8286 3377 5657 22868 22870 1551 1553 26201 26375 6394 14686 14687 26817 2903 10287 16363 11145 5246 5250 14737 23734 23730 21861 21859 26687 29894 30434 30431 2899 2902 16334 5302 5298 9888 4303 10265 22367 18580 14695 27846 17626 2109 6052 16127 30216 4367 6687 26267 24728 24730 14722 14720 1445 27700 27697 1322 18938 17173 17172 14492 24191 26309 26311 18431 18429 22637 22639 1746 841 19542 25007 23073 921 8727 22508 11259 2295 28478 17819 26866 29146 1507 7960 7961 11492 26369 26371 18436 5241 24911 10101 10102 7319 7323 10634 18983 29268 29265 26149 26150 21925 21927 17972 18001 20748 20747 23042 30325 19845 24599 4808 29229 14641 14643 6370 15708 15710 29633 29632 21113 21114 11209 11213 22426 22424 29203 29204 29502 29488 4378 26546 26549 4062 18589 26724 6332 23821 27135 22196 16034 11065 11709 23015 18600 2580 29261 27119 27964 27971 11480 11481 9572 17430 17428 9575 7945 14729 8825 26717 26720 9302 9326 18620 924 27200 20233 10699 27257 26880 26881 12995 17825 17823 24741 22069 19432 19359 13970 3496 1711 23383 21158 12866 30263 18787 26538 14868 4035 4388 10801 10632 25632 23963 28612 23253 27927 1178 29132 20213 1016 14461 24758 23386 21388 5313 5058 28289 4759 4761 4762 2437 12185 12187 18988 1713 28792 18380 15839 14194 18840 4330 4864 8121 9335 10310 10638 18392 21281 20942 20443 26148 20072 21300 12484 2275 25950 3671 29507 16628 10059 2250 1723 882 29614 22890 7292 3148 16143 24227 8787 10741 1326 5613 9289 9306 865 6419 4798 13777 13774 17747 17712 708 16833 3004 17056 6800 2653 20042 17162 26198 26200 27852 24966 24968 11426 30306 30308 5191 6541 20215 20217 1772 3268 4046 4053 4050 3207 3027 3022 4057 3074 3029 3173 3168 12543 10664 21634 17128 6401 12365 8519 13988 13986 30242 15429 9261 23736 7773 12871 20211 20212 2210 10272 16332 16353 5091 25709 22283 2518 559 3861 19815 28848 16627 1790 20457 593: 23100 8437 16789 9184 9170 14972 26126 2782 2808 8912 12593 5659 27751 17249 847 16077 17003 17564 17566 9675 16458 25308 11810 6462 19004 23303 25333 8046 1432 22200 23141 1516 3596 26032 1858 3259 28746 25829 23426 25373 17115 18882 24257 4938 22448 11228 22286 22389 18549 21796 28404 16829 23612 23617 23616 23645 23590 25680 25614 3975 18943 21410 15360 23410 8549 26330 4056 30346 24472 24445 15829 27029 27626 7896 28162 7743 11962 15101 26380 30303 26492 1890 15003 15005 17406 17853 5309 7867 3683 23220 12178 1817 12021 3159 5110 21308 29714 30354 28815 2223 12072 23205 2188 19401 16746 23172 5164 19927 20771 7518 23417 13391 12324 29494 4043 27813 29038 29780 28610 19153 7533 13762 4157 16421 4895 27867 25304 17568 17567 21063 16780 13258 11850 1334 24652 24325 18753 5836 16750 11824 20390 3170 13418 12249 20037 15769 5466 11682 25338 15918 9169 14001 3135 16677 18384 2213 9831 9001 2847 20465 14307 20286 10381 14305 30233 20568 24612 28359 13523 11725 13899 677 3809 24421 12358 12047 11941 29944 10425 20270 7425 12223 22959 25148 9300 8277 29986 21518 16545 25208 26145 594: 14081 8646 19510 3201 2969 21123 15598 14545 3412 24368 6958 8607 10353 595: 3687 13637 6857 13434 15892 15230 25954 18782 18783 18779 26319 3515 1014 21404 29758 1644 27147 15850 24399 9128 9154 16774 3773 27893 20486 12084 13600 29024 13597 29026 12676 4516 12392 10606 3631 16048 10151 20647 7798 14866 22177 6793 19027 4906 27511 7809 25075 26399 26044 1108 21212 3720 19569 14929 10537 11077 24782 21269 13233 23192 10539 24375 28382 7724 29220 7674 24131 28806 6795 28135 6830 26699 14196 28182 7465 6291 15138 29628 1123 15229 14863 15755 2030 14862 14269 17078 9228 4792 13137 8362 6931 8252 3767 14734 2995 13859 1957 3616 12222 2724 8691 15141 20150 4991 22712 22160 13892 14933 18671 18647 3672 8714 21442 25038 11854 6682 26742 6623 12833 1237 10466 10469 886 26275 17293 25839 20091 13855 18348 5981 13646 12691 10633 15139 596: 11135 17513 29853 2950 5458 29779 20336 13241 4799 29016 17076 11780 4104 12952 11732 12095 4999 16170 5457 3045 25718 6165 16051 8403 18273 6347 3040 24142 6392 3814 4226 20621 13649 27722 19640 9479 26129 15632 8041 25934 21263 12094 3514 30043 15134 24774 25723 29058 14294 10387 22923 13706 8226 14883 18231

Example 7. Selection of Transgenic Plants with Enhanced Agronomic Trait(s)

This example illustrates identification of plant cells of the invention by screening derived plants and seeds for enhanced trait. Transgenic seed and plants in corn, soybean, cotton or canola with recombinant DNA constructs identified in Table 2 are prepared by plant cells transformed with DNA that is stably integrated into the genome of the corn cell. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as compared to control plants

A. Selection for Enhanced Nitrogen Use Efficiency

Transgenic corn seeds provided by the present invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). A variety of physiological traits are monitored. Plants with enhanced NUE provide higher yield as compared to control plants.

B. Selection for Increased Yield

Effective selection of enhanced yielding transgenic plants uses hybrid progeny of the transgenic plants for corn, cotton, and canola, or inbred progeny of transgenic plants for soybeanplants plant such as corn, cotton, canola, or inbred plant such as soy, canola and cottoncotton over multiple locations with plants grown under optimal production management practices, and maximum pest control. A useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods may be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons, to statistically distinguish yield improvement from natural environmental effects.

In one field trial, transgenic corn plants comprising corn G1543 like 2 transgene as set forth in NUC SEQ ID NO: 74 under a tissue preferred promoter, such as green tissue promoter, have been shown to have an increased yield.

C. Selection for Enhanced Water Use Efficiency (WUE)

The selection process imposes a water withholding period to induce stress drought followed by watering. For example, for corn, a useful selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle. The primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment.

D. Selection for Growth Under Cold Stress

(1) Cold germination assay—Trays of transgenic and control seeds are placed in a growth chamber at 9.7° C. for 24 days (no light). Seeds having higher germination rates as compared to the control are identified.

(2) Cold field efficacy trial—A cold field efficacy trial is used to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.

Seed emergence is defined as the point when the growing shoot breaks the soil surface. The number of emerged seedlings in each plot is counted everyday from the day the earliest plot begins to emerge until no significant changes in emergence occur. In addition, for each planting date, the latest date when emergence is 0 in all plots is also recorded. Seedling vigor is also rated at V3-V4 stage before the average of corn plant height reaches 10 inches, with 1=excellent early growth, 5=Average growth and 9=poor growth. Days to 50% emergence, maximum percent emergence and seedling vigor are used to determine plants with enhanced cold tolerance.

E. Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels

This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample (Table 9). Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan. An NIR calibration for the analytes of interest is used to predict the values of an unknown sample. The NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides predicted values as well as information on how well the sample fits in the calibration.

Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.

TABLE 9 Typical sample(s): Whole grain corn and soybean seeds Analytical time to run Less than 0.75 min per sample method: Total elapsed time per run: 1.5 minute per sample Typical and minimum sample Corn typical: 50 cc; minimum 30 cc size: Soybean typical: 50 cc; minimum 5 cc Typical analytical range: Determined in part by the specific calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.

Example 8. Consensus Sequence

This example illustrates the identification of consensus amino acid sequence for the proteins and homologs encoded by DNA that is used to prepare the transgenic seed and plants of this invention having enhanced agronomic traits.

ClustalW program was selected for multiple sequence alignments of the amino acid sequence of SEQ ID NO: 301 and its 20 homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. FIG. 1 shows the sequences of SEQ ID NO: 301, its homologs and the consensus sequence (SEQ ID NO: 30526) at the end. The symbols for consensus sequence are (1) uppercase letters for 100% identity in all positions of multiple sequence alignment output; (2) lowercase letters for >=70% identity; symbol; (3) “X” indicated <70% identity; (4) dashes “-” meaning that gaps were in >=70% sequences.

The consensus amino acid sequence can be used to identify DNA corresponding to the full scope of this invention that is useful in providing transgenic plants, for example corn and soybean plants with enhanced agronomic traits, for example improved nitrogen use efficiency, improved yield, improved water use efficiency and/or improved growth under cold stress, due to the expression in the plants of DNA encoding a protein with amino acid sequence identical to the consensus amino acid sequence.

Example 9. Identification of Amino Acid Domain by Pfam Analysis

This example illustrates the identification of domain and domain module by Pfam analysis.

The amino acid sequence of the expressed proteins that are shown to be associated with an enhanced trait are analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software in the appended computer listing. The Pfam protein domains and modules for the proteins of SEQ ID NO: 299 through 596 are shown in Tables 10, 11 and 12. The Hidden Markov model databases for the identified patent families are also in the appended computer listing allowing identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 299 is characterized by three Pfam domains, i.e. KNOX1, KNOX2 and ELK.

TABLE 10 Pfam annotation PEP SEQ ID NO Gene ID Pfam domain name Begin Stop Score E-value 299 PHE0007721_18998.pep KNOX1 102 146 90.4 5.50E−24 299 PHE0007721_18998.pep KNOX2 153 204 101.2 3.10E−27 299 PHE0007721_18998.pep ELK 242 263 37 6.50E−08 300 PHE0007756_18009.pep RPE65 105 591 864  7.30E−257 302 PHE0004988_15925.pep F-box 4 52 23.7 0.00064 302 PHE0004988_15925.pep LRR_1 157 179 9.7 4.4 302 PHE0004988_15925.pep LRR_2 290 314 14.1 0.19 303 PHE0007140_21771.pep MtN3_slv 9 98 98.2 2.50E−26 303 PHE0007140_21771.pep MtN3_slv 134 221 73.6 6.20E−19 304 PHE0006823_16403.pep Globin 10 149 102.6 1.10E−27 305 PHE0007440_22555.pep Miro 14 128 88.4 2.20E−23 305 PHE0007440_22555.pep Ras 14 175 332.3 8.40E−97 306 PHE0000206_22432.pep Pkinase 79 337 342.2  8.80E−100 306 PHE0000206_22432.pep efhand 384 412 25 0.00026 306 PHE0000206_22432.pep efhand 456 484 24.9 0.00028 306 PHE0000206_22432.pep efhand 490 518 35.1 2.40E−07 307 PHE0000598_16824.pep HLH 385 434 54.6 3.30E−13 308 PHE0007590_17883.pep S1 2 70 92.7 1.10E−24 309 PHE0007588_17881.pep S1 2 86 73.5 6.50E−19 310 PHE0007592_17885.pep S1 1 75 48 3.20E−11 311 PHE0007587_17880.pep S1 3 75 106.6 7.10E−29 312 PHE0007624_17923.pep S1 2 72 45.6 1.70E−10 312 PHE0007624_17923.pep eIf-1a 5 70 134.9 2.20E−37 313 PHE0007591_17884.pep S1 2 68 63.9 5.20E−16 314 PHE0007623_17922.pep CN_hydrolase 11 184 166.3 7.50E−47 315 PHE0007583_17871.pep MtN3_slv 9 98 102.2 1.50E−27 315 PHE0007583_17871.pep MtN3_slv 132 218 112.8 1.00E−30 316 PHE0006618_16146.pep S10_plectin 3 98 240.6 3.40E−69 317 PHE0006791_16374.pep GUN4 84 227 308.7 1.00E−89 318 PHE0007620_17918.pep peroxidase 89 321 192.4 1.10E−54 319 PHE0006659_16195.pep MFS_1 10 391 111.5 2.50E−30 321 PHE0006274_15867.pep E2F_TDP 130 195 135.8 1.10E−37 322 PHE0006637_16166.pep PP2C 7 305 255.6 1.00E−73 323 PHE0006926_16815.pep VPS28 18 209 281.8 1.40E−81 324 PHE0006821_16402.pep PALP 49 358 −65.8 0.00015 325 PHE0007687_18057.pep p450 35 462 124 4.20E−34 326 PHE0007642_17999.pep PAS 186 300 15.6 0.014 326 PHE0007642_17999.pep PAS_3 211 303 25.3 0.00022 326 PHE0007642_17999.pep PAS 464 578 17.8 0.0089 326 PHE0007642_17999.pep PAS_3 489 581 23.5 0.00052 326 PHE0007642_17999.pep Pkinase 663 952 269.7 5.80E−78 327 PHE0007677_18052.pep FAD_binding_3 5 372 −96.1 4.10E−05 328 PHE0007644_18001.pep LRRNT_2 23 64 49.2 1.40E−11 328 PHE0007644_18001.pep LRR_1 97 119 10.5 3.1 328 PHE0007644_18001.pep LRR_1 121 143 14.4 0.42 328 PHE0007644_18001.pep LRR_1 145 167 12.1 1.5 328 PHE0007644_18001.pep LRR_1 169 192 13 1.1 328 PHE0007644_18001.pep LRR_1 194 216 14.1 0.52 328 PHE0007644_18001.pep Pkinase 414 716 57.1 5.60E−14 329 PHE0007640_17992.pep CorA 66 448 438.4  9.30E−129 330 PHE0007678_18053.pep 4HBT 66 151 56.4 9.40E−14 331 PHE0007649_18006.pep Ank 108 140 50.4 6.20E−12 331 PHE0007649_18006.pep Pkinase 196 455 113 8.80E−31 331 PHE0007649_18006.pep Pkinase_Tyr 196 455 94.9 2.40E−25 332 PHE0006726_16298.pep WD40 45 83 30.2 7.30E−06 332 PHE0006726_16298.pep WD40 135 173 38.6 2.10E−08 333 PHE0006218_8776.pep Pyr_redox_2 85 370 163.7 4.70E−46 333 PHE0006218_8776.pep Pyr_redox 231 325 93.9 4.80E−25 333 PHE0006218_8776.pep Thioredoxin 423 528 25 1.50E−06 333 PHE0006218_8776.pep Glutaredoxin 446 508 27.6 4.30E−05 335 PHE0002554_17876.pep Chloroa_b-bind 63 261 263.3 5.00E−76 336 PHE0006807_16388.pep CCT 352 390 76 1.20E−19 337 PHE0003359_8487.pep p450 51 489 120.5 4.90E−33 338 PHE0006542_15765.pep PMSR 92 245 271 2.30E−78 339 PHE0007622_17921.pep Spermine_synth 34 279 249.7 6.10E−72 340 PHE0007630_17956.pep 2OG-FeII_Oxy 190 291 149.7 7.90E−42 341 PHE0007593_17886.pep Spermine_synth 28 273 503.6  2.20E−148 342 PHE0006475_15588.pep PsbQ 3 162 209.5 7.60E−60 343 PHE0007619_17915.pep MBD 11 84 65.4 1.80E−16 344 PHE0006846_16447.pep Sterol_desat 1 186 76.3 9.30E−20 345 PHE0007584_17874.pep MBD 4 77 81.3 3.00E−21 346 PHE0003695_17913.pep LRRNT_2 23 64 41.6 2.80E−09 346 PHE0003695_17913.pep LRR_1 93 115 14.3 0.45 346 PHE0003695_17913.pep LRR_1 117 139 18.3 0.028 346 PHE0003695_17913.pep LRR_1 141 163 9.2 5.5 346 PHE0003695_17913.pep LRR_1 165 186 12.7 1.2 346 PHE0003695_17913.pep LRR_1 189 211 10.1 3.6 346 PHE0003695_17913.pep LRR_1 213 235 9.8 4.3 346 PHE0003695_17913.pep LRR_1 237 259 14.8 0.32 346 PHE0003695_17913.pep LRR_1 260 281 10.6 2.9 346 PHE0003695_17913.pep LRR_1 284 306 17.4 0.053 346 PHE0003695_17913.pep LRR_1 308 330 13.8 0.65 346 PHE0003695_17913.pep LRR_1 332 354 19.3 0.014 346 PHE0003695_17913.pep LRR_1 356 378 9 5.8 346 PHE0003695_17913.pep LRR_1 380 402 15.7 0.17 346 PHE0003695_17913.pep LRR_1 404 426 11.8 1.8 346 PHE0003695_17913.pep LRR_1 428 450 18.8 0.02 346 PHE0003695_17913.pep LRR_1 452 474 13.2 0.93 346 PHE0003695_17913.pep LRR_1 476 498 13.1 1 346 PHE0003695_17913.pep LRR_1 500 521 10.4 3.3 346 PHE0003695_17913.pep LRR_1 523 542 14.4 0.42 346 PHE0003695_17913.pep Pkinase 648 917 111.8 2.00E−30 346 PHE0003695_17913.pep Pkinase_Tyr 648 914 90.4 5.40E−24 347 PHE0003695_17879.pep LRRNT_2 23 64 41.6 2.80E−09 347 PHE0003695_17879.pep LRR_1 93 115 14.3 0.45 347 PHE0003695_17879.pep LRR_1 117 139 18.3 0.028 347 PHE0003695_17879.pep LRR_1 141 163 9.2 5.5 347 PHE0003695_17879.pep LRR_1 165 186 12.7 1.2 347 PHE0003695_17879.pep LRR_1 189 211 10.1 3.6 347 PHE0003695_17879.pep LRR_1 213 235 9.8 4.3 347 PHE0003695_17879.pep LRR_1 237 259 14.8 0.32 347 PHE0003695_17879.pep LRR_1 260 281 10.6 2.9 347 PHE0003695_17879.pep LRR_1 284 306 17.4 0.053 347 PHE0003695_17879.pep LRR_1 308 330 13.8 0.65 347 PHE0003695_17879.pep LRR_1 332 354 19.3 0.014 347 PHE0003695_17879.pep LRR_1 356 378 9 5.8 347 PHE0003695_17879.pep LRR_1 380 402 15.7 0.17 347 PHE0003695_17879.pep LRR_1 404 426 11.8 1.8 347 PHE0003695_17879.pep LRR_1 428 450 18.8 0.02 347 PHE0003695_17879.pep LRR_1 452 474 13.2 0.93 347 PHE0003695_17879.pep LRR_1 476 498 13.1 1 347 PHE0003695_17879.pep LRR_1 500 521 10.4 3.3 347 PHE0003695_17879.pep LRR_1 523 542 14.4 0.42 347 PHE0003695_17879.pep Pkinase 648 917 111.8 2.00E−30 347 PHE0003695_17879.pep Pkinase_Tyr 648 914 90.4 5.40E−24 349 PHE0007645_18002.pep AP2 115 180 156.4 7.20E−44 350 PHE0006784_16366.pep PALP 12 301 453.6  2.50E−133 351 PHE0006171_16491.pep Glyoxalase 70 214 136.8 5.90E−38 353 PHE0006906_16796.pep Proteasome 10 206 145.9 1.00E−40 354 PHE0006649_16180.pep AP2 46 110 149.5 8.60E−42 355 PHE0006809_16390.pep Prismane 1 548 886.8  9.80E−264 356 PHE0006918_16808.pep SWIM 321 353 42.8 1.10E−09 357 PHE0007813_18219.pep MtN3_slv 9 98 79.8 8.50E−21 357 PHE0007813_18219.pep MtN3_slv 132 218 125.3 1.80E−34 359 PHE0006825_16405.pep Cytochrom_C552 27 476 1333.6 0 360 PHE0006964_16864.pep tRNA_anti 43 122 55.2 2.10E−13 360 PHE0006964_16864.pep tRNA-synt_2 140 557 208.2 1.90E−59 361 PHE0008105_18407.pep Histone 152 225 69.9 8.40E−18 361 PHE0008105_18407.pep CBFD_NFYB_HMF 158 222 77.9 3.10E−20 362 PHE0006630_16159.pep Ldh_1_N 90 239 202 1.30E−57 362 PHE0006630_16159.pep Ldh_1_C 241 413 258.1 1.80E−74 363 PHE0006966_16868.pep DNA_photolyase 12 183 298.7 1.10E−86 363 PHE0006966_16868.pep FAD_binding_7 214 492 536.3  3.30E−158 365 PHE0006608_16123.pep GSHPx 42 150 237.8 2.30E−68 366 PHE0010462_21459.pep NUDIX 17 159 111.7 2.20E−30 366 PHE0010462_21459.pep NUDIX 190 322 100.5 4.90E−27 367 PHE0009211_21774.pep Auxin_inducible 1 106 149.5 8.80E−42 368 PHE0006256_8775.pep RPE65 105 591 864.5  5.10E−257 369 PHE0006989_16918.pep Pkinase 88 396 224.8 1.90E−64 370 PHE0007649_18166.pep Ank 108 140 50.4 6.20E−12 370 PHE0007649_18166.pep Pkinase 196 455 115.1 2.00E−31 370 PHE0007649_18166.pep Pkinase_Tyr 196 455 98.9 1.50E−26 371 PHE0006708_16264.pep DEAD 57 223 202.7 8.40E−58 371 PHE0006708_16264.pep Helicase_C 291 367 127.8 3.10E−35 372 PHE0001117_19094.pep Homeobox 79 133 68.2 2.70E−17 372 PHE0001117_19094.pep HALZ 134 178 66.7 7.20E−17 373 PHE0006266_8814.pep Fe_bilin_red 16 244 209.5 7.50E−60 374 PHE0006795_16378.pep Na_H_antiport_1 4 380 875.9  1.90E−260 375 PHE0006956_16853.pep Molybdop_Fe4S4 2 56 92 1.90E−24 375 PHE0006956_16853.pep Molybdopterin 59 482 377.8  1.60E−110 375 PHE0006956_16853.pep Molydop_binding 578 689 159.8 7.10E−45 375 PHE0006956_16853.pep Fer2_BFD 825 877 62 2.00E−15 377 PHE0006824_16404.pep Globin 14 154 93.4 7.00E−25 378 PHE0006812_16393.pep Bac_globin 3 118 188.4 1.70E−53 379 PHE0006815_16396.pep Bac_globin 26 146 191.4 2.10E−54 380 PHE0006806_16387.pep Bac_globin 26 146 196.8 5.10E−56 381 PHE0006624_16153.pep NAD_binding_2 3 178 282.5 7.90E−82 381 PHE0006624_16153.pep 6PGD 182 473 713.8  1.20E−211 382 PHE0005006_15823.pep Chloroa_b-bind 63 242 241.4 1.90E−69 384 PHE0006683_16229.pep Response_reg 10 151 73.8 5.40E−19 385 PHE0006884_16703.pep Glyco_transf_5 83 344 462.7  4.80E−136 385 PHE0006884_16703.pep Glycos_transf_1 384 567 40.2 7.10E−09 386 PHE0006691_16237.pep NAD_Gly3P_dh_N 6 165 285 1.40E−82 386 PHE0006691_16237.pep ApbA 8 169 6.6 0.00011 386 PHE0006691_16237.pep NAD_Gly3P_dh_C 183 327 289.1 8.20E−84 387 PHE0006790_16372.pep Rieske 220 317 96.7 7.10E−26 387 PHE0006790_16372.pep PaO 408 507 180.7 3.60E−51 388 PHE0009143_19932.pep Histone_HNS 21 129 170.1 5.70E−48 389 PHE0008406_18830.pep AA_permease 57 511 619.8  2.40E−183 390 PHE0008279_18708.pep Mit_rib_S27 14 93 135.3 1.70E−37 391 PHE0009142_19931.pep Histone_HNS 21 130 175.1 1.70E−49 393 PHE0007639_17991.pep ELFV_dehydrog_N 84 214 298.9 9.20E−87 393 PHE0007639_17991.pep ELFV_dehydrog 229 474 469.7  3.60E−138 394 PHE0007646_18170.pep F-box 36 83 51.8 2.20E−12 394 PHE0007646_18170.pep Kelch_1 131 185 25.1 0.00026 394 PHE0007646_18170.pep Kelch_1 187 233 44.2 4.40E−10 394 PHE0007646_18170.pep Kelch_2 187 233 26.1 0.00012 395 PHE0007765_18182.pep GST_N 5 79 69.6 1.00E−17 395 PHE0007765_18182.pep GST_C 101 204 28.8 1.90E−05 396 PHE0008167_18465.pep Pkinase 8 262 210 5.60E−60 396 PHE0008167_18465.pep Pkinase_Tyr 8 262 247.9 2.10E−71 398 PHE0008183_18479.pep LRRNT_2 23 66 49.3 1.30E−11 398 PHE0008183_18479.pep LRR_1 71 93 12.1 1.6 398 PHE0008183_18479.pep LRR_1 95 117 10.3 3.3 398 PHE0008183_18479.pep LRR_1 119 142 13 1 398 PHE0008183_18479.pep LRR_1 144 166 19.5 0.012 398 PHE0008183_18479.pep LRR_1 168 190 10.6 3 398 PHE0008183_18479.pep LRR_1 192 214 8.8 6.4 398 PHE0008183_18479.pep LRR_1 289 311 17.3 0.055 398 PHE0008183_18479.pep LRR_1 313 335 10.6 2.9 398 PHE0008183_18479.pep LRR_1 337 359 10.8 2.8 398 PHE0008183_18479.pep LRR_1 361 384 12 1.6 398 PHE0008183_18479.pep LRR_1 409 431 10.4 3.2 398 PHE0008183_18479.pep LRR_1 457 479 11.9 1.7 398 PHE0008183_18479.pep LRR_1 481 503 10.2 3.4 398 PHE0008183_18479.pep LRR_1 505 527 10.4 3.3 398 PHE0008183_18479.pep LRR_1 529 551 10.9 2.6 398 PHE0008183_18479.pep LRR_1 553 575 9.3 5.2 398 PHE0008183_18479.pep LRR_1 577 598 11 2.4 398 PHE0008183_18479.pep Pkinase 695 966 133.8 4.80E−37 398 PHE0008183_18479.pep Pkinase_Tyr 695 966 134.8 2.30E−37 399 PHE0007585_17875.pep LEA_3 2 98 138.9 1.30E−38 400 PHE0006804_16385.pep zf-CCCH 13 39 35.4 1.90E−07 400 PHE0006804_16385.pep zf-CCCH 149 174 24.3 0.00045 401 PHE0006703_15751.pep PFK 72 347 650.2  1.70E−192 402 PHE0007410_17653.pep Acyltransferase 27 249 29.2 1.00E−05 403 PHE0006854_16456.pep YABBY 40 278 249.1 9.30E−72 404 PHE0007721_21293.pep KNOX1 102 146 90.4 5.50E−24 404 PHE0007721_21293.pep KNOX2 153 204 101.2 3.10E−27 404 PHE0007721_21293.pep ELK 242 263 37 6.50E−08 405 PHE0006563_15990.pep GATase_2 2 161 103.9 4.70E−28 405 PHE0006563_15990.pep Asn_synthase 209 450 328.7 9.80E−96 406 PHE0006619_16147.pep AA_kinase 15 261 192.3 1.20E−54 407 PHE0006813_16394.pep Bac_globin 7 124 123 8.50E−34 408 PHE0006688_16234.pep Ribosomal_S2 13 229 448.6  8.00E−132 409 PHE0006635_16164.pep MGS 28 121 99.4 1.10E−26 411 PHE0008416_18838.pep PTR2 115 504 350.4  3.00E−102 413 PHE0008599_19166.pep Isoamylase_N 24 115 93.4 6.60E−25 413 PHE0008599_19166.pep Alpha-amylase 164 578 75.8 1.40E−19 414 PHE0008375_18732.pep Pribosyltran 93 237 141.8 1.80E−39 416 PHE0008394_18763.pep Gln-synt_N 68 148 147.3 4.20E−41 416 PHE0008394_18763.pep Gln-synt_C 154 406 287.7 2.20E−83 417 PHE0008395_18764.pep Gln-synt_N 68 148 147.3 4.20E−41 417 PHE0008395_18764.pep Gln-synt_C 154 406 285 1.50E−82 418 PHE0008444_18846.pep Gln-synt_N 17 97 150.4 4.70E−42 418 PHE0008444_18846.pep Gln-synt_C 103 355 283.9 3.00E−82 419 PHE0006819_16400.pep Lactamase_B 47 236 77.1 5.60E−20 419 PHE0006819_16400.pep Flavodoxin_1 267 397 8.1 0.0041 419 PHE0006819_16400.pep Flavin_Reduct 424 573 254.7 1.90E−73 420 PHE0007417_17663.pep EIN3 60 467 777.5  7.80E−231 421 PHE0008443_18845.pep GATase_2 2 161 98.7 1.70E−26 421 PHE0008443_18845.pep Asn_synthase 209 450 331 2.00E−96 422 PHE0006818_16399.pep Lactamase_B 34 227 105.3 1.80E−28 422 PHE0006818_16399.pep Flavodoxin_1 256 389 86.4 8.80E−23 422 PHE0006818_16399.pep Rubredoxin 423 471 89.8 8.10E−24 423 PHE0006579_16031.pep Thi4 63 306 552.2  5.40E−163 423 PHE0006579_16031.pep DAO 91 319 −9 1.90E−05 424 PHE0006808_16389.pep CCT 354 392 75.3 1.90E−19 425 PHE0008160_18460.pep TPP_enzyme_N 45 221 286.5 5.20E−83 425 PHE0008160_18460.pep TPP_enzyme_M 243 376 82.1 1.70E−21 425 PHE0008160_18460.pep TPP_enzyme_C 431 578 34.8 2.80E−09 426 PHE0007571_17834.pep GSH_synth_ATP 29 499 836.5  1.30E−248 426 PHE0007571_17834.pep GSH_synthase 229 331 200 5.50E−57 427 PHE0007586_17877.pep Chloroa_b-bind 64 261 255.3 1.20E−73 429 PHE0009729_21717.pep Homeobox 67 123 68.9 1.60E−17 429 PHE0009729_21717.pep HALZ 124 168 53.4 7.60E−13 430 PHE0006424_15520.pep PsbW_2 1 133 382.1  8.60E−112 431 PHE0006392_15480.pep PsbP 106 322 252.9 6.50E−73 432 PHE0006589_16093.pep Thioredoxin 64 167 130.3 5.20E−36 433 PHE0009258_21487.pep Na_H_Exchanger 22 441 181.7 1.70E−51 434 PHE0006680_16226.pep 2OG-FeII_Oxy 187 287 158 2.40E−44 435 PHE0006481_16072.pep adh_short 33 181 28.8 7.00E−08 436 PHE0006269_8820.pep TPR_1 74 107 21.3 0.0035 436 PHE0006269_8820.pep TPR_2 74 107 24.7 0.00034 436 PHE0006269_8820.pep TPR_1 108 141 37.4 4.80E−08 436 PHE0006269_8820.pep TPR_2 108 141 35.3 2.10E−07 436 PHE0006269_8820.pep TPR_1 142 175 15 0.086 436 PHE0006269_8820.pep TPR_2 142 175 23.8 0.00063 436 PHE0006269_8820.pep TPR_1 179 212 7.9 0.61 436 PHE0006269_8820.pep TPR_4 247 272 23.6 0.00069 436 PHE0006269_8820.pep TPR_1 281 314 16.2 0.063 436 PHE0006269_8820.pep TPR_2 281 314 26 0.00014 436 PHE0006269_8820.pep TPR_1 349 382 13.6 0.13 437 PHE0006783_16365.pep Aa_trans 32 469 574.9  7.90E−170 438 PHE0003151_18392.pep AP2 318 391 149.5 8.70E−42 438 PHE0003151_18392.pep AP2 420 485 125.8 1.20E−34 439 PHE0008272_18723.pep HSF_DNA-bind 18 188 213.9 3.50E−61 440 PHE0008277_18706.pep SNF5 172 400 471.8  8.60E−139 441 PHE0008109_18411.pep Sad1_UNC 203 330 195.6 1.10E−55 442 PHE0008280_18826.pep Alpha-amylase 14 452 198.9 1.20E−56 443 PHE0002424_15825.pep adh_short 43 215 24.9 1.30E−07 443 PHE0002424_15825.pep KR 43 200 −69.1 0.0024 444 PHE0006914_16804.pep AAA 204 391 298.6 1.10E−86 445 PHE0006642_16172.pep p450 42 496 213.5 4.80E−61 447 PHE0009926_21079.pep DSPc 24 152 137.5 3.60E−38 448 PHE0006206_19159.pep Sina 106 305 426.4  4.00E−125 449 PHE0008274_18705.pep BURP 56 280 380  3.60E−111 450 PHE0009510_20526.pep Spermine_synth 38 283 500.4  2.10E−147 451 PHE0009937_21097.pep Spermine_synth 38 283 500.4  2.10E−147 452 PHE0009927_21080.pep DSPc 24 162 146.6 6.60E−41 454 PHE0006445_15956.pep Allene_ox_cyc 74 253 401.6  1.20E−117 455 PHE0006987_16893.pep efhand 86 114 25 0.00026 455 PHE0006987_16893.pep efhand 167 195 27.6 4.30E−05 456 PHE0004230_15865.pep E2F_TDP 146 211 133.8 4.60E−37 457 PHE0006814_16395.pep Bac_globin 26 144 206 8.80E−59 458 PHE0002773_15881.pep NTP_transferase 88 366 415.4  8.30E−122 459 PHE0006060_15842.pep ubiquitin 5 73 138 2.50E−38 459 PHE0006060_15842.pep ubiquitin 81 149 138 2.50E−38 459 PHE0006060_15842.pep ubiquitin 157 225 138 2.50E−38 459 PHE0006060_15842.pep ubiquitin 233 301 138 2.50E−38 460 PHE0006850_16451.pep YABBY 6 166 342.9  5.20E−100 461 PHE0008043_18199.pep Homeobox 25 85 64.6 3.20E−16 461 PHE0008043_18199.pep START 164 374 198.3 1.80E−56 461 PHE0008043_18199.pep MEKHLA 693 840 296.7 4.40E−86 462 PHE0000125_18852.pep Response_reg 28 153 25.4 3.80E−05 462 PHE0000125_18852.pep CCT 457 495 70.6 5.10E−18 463 PHE0008269_18720.pep Pkinase 23 279 234 3.30E−67 464 PHE0008264_18712.pep zf-UBR 40 109 73.4 7.10E−19 465 PHE0002782_20059.pep PGI 2 457 172.8 8.80E−49 466 PHE0009438_20404.pep GATA 191 226 72.7 1.10E−18 467 PHE0009429_20392.pep ParBc 70 151 47.5 4.50E−11 468 PHE0009440_20406.pep ParBc 11 126 55.3 2.00E−13 469 PHE0008543_18945.pep TP_methylase 222 435 272.6 7.70E−79 470 PHE0006960_16857.pep Oxidored_molyb 116 301 289.2 7.70E−84 470 PHE0006960_16857.pep Mo-co_dimer 326 459 300.9 2.30E−87 470 PHE0006960_16857.pep Cyt-b5 515 588 93.3 7.20E−25 470 PHE0006960_16857.pep FAD_binding_6 633 740 212.6 9.20E−61 470 PHE0006960_16857.pep NAD_binding_1 759 872 169.6 8.00E−48 471 PHE0009427_20389.pep IGPD 103 247 372.6  6.20E−109 472 PHE0006437_15906.pep Pkinase 39 307 15.8 1.70E−09 473 PHE0007409_17652.pep DAGAT 64 340 278.2 1.60E−80 474 PHE0009426_20387.pep PHP 2 281 104.4 3.30E−28 475 PHE0009430_20393.pep ParBc 44 128 45.7 1.60E−10 476 PHE0007003_16906.pep PTPA 96 396 524  1.60E−154 477 PHE0008378_18741.pep bZIP_1 223 280 76.5 8.20E−20 477 PHE0008378_18741.pep bZIP_2 224 277 47.5 4.40E−11 478 PHE0008273_18725.pep zf-CCCH 80 106 39.3 1.30E−08 479 PHE0008547_18953.pep Fer2 20 95 95 2.20E−25 480 PHE0006922_16812.pep Hexokinase_1 44 251 260.7 2.90E−75 480 PHE0006922_16812.pep Hexokinase_2 258 501 261.2 2.10E−75 481 PHE0006920_16810.pep AAA 267 458 270 4.60E−78 481 PHE0006920_16810.pep Vps4_C 464 514 4.5 0.00031 482 PHE0008396_18765.pep Gln-synt_N 68 148 147.3 4.20E−41 482 PHE0008396_18765.pep Gln-synt_C 154 406 285.4 1.10E−82 483 PHE0006957_16854.pep Gln-synt_N 68 148 147.3 4.20E−41 483 PHE0006957_16854.pep Gln-synt_C 154 406 285.4 1.10E−82 484 PHE0006404_15936.pep RRM_1 8 77 81.4 2.80E−21 484 PHE0006404_15936.pep RRM_1 112 182 81.8 2.10E−21 485 PHE0006820_16401.pep Lactamase_B 47 236 82.8 1.10E−21 485 PHE0006820_16401.pep Flavin_Reduct 423 572 222.8 7.90E−64 486 PHE0006690_16236.pep MFS_1 57 421 44.3 4.30E−10 487 PHE0006395_15932.pep LRR_1 185 206 11.9 1.7 487 PHE0006395_15932.pep LRR_1 208 229 17.1 0.065 487 PHE0006395_15932.pep LRR_1 231 252 13.5 0.77 487 PHE0006395_15932.pep LRR_1 254 272 12.6 1.2 487 PHE0006395_15932.pep LRR_1 278 299 8.4 7.8 487 PHE0006395_15932.pep LRR_1 349 370 20.8 0.0049 487 PHE0006395_15932.pep LRR_1 372 394 7.8 9.8 488 PHE0006759_16384.pep SHMT 55 453 1032.6 0 489 PHE0006576_16028.pep Myb_DNA-binding 11 57 59.3 1.30E−14 489 PHE0006576_16028.pep Myb_DNA-binding 63 108 48.9 1.70E−11 490 PHE0006979_16885.pep Tryp_alpha_amyl 33 111 55.3 2.00E−13 491 PHE0009786_21754.pep HLH 33 80 30 8.20E−06 492 PHE0006572_16007.pep Pkinase 11 269 317 3.30E−92 494 PHE0006588_16092.pep Thioredoxin 56 161 128.8 1.50E−35 495 PHE0006985_16891.pep DUF1716 13 118 159.3 1.00E−44 496 PHE0006875_16688.pep PSI_PSAK 44 138 191.6 1.90E−54 497 PHE0006626_16155.pep Glyco_hydro_17 30 335 587.5  1.20E−173 498 PHE0006689_16235.pep Aa_trans 165 548 224.1 3.20E−64 499 PHE0006799_16382.pep B12-binding 10 135 104.3 3.70E−28 499 PHE0006799_16382.pep Radical_SAM 202 368 91.2 3.10E−24 500 PHE0006959_16856.pep Oxidored_molyb 143 328 286.7 4.40E−83 500 PHE0006959_16856.pep Mo-co_dimer 353 486 297.6 2.40E−86 500 PHE0006959_16856.pep Cyt-b5 543 616 90.4 5.60E−24 500 PHE0006959_16856.pep FAD_binding_6 660 767 231.6 1.70E−66 500 PHE0006959_16856.pep NAD_binding_1 786 899 186.4 7.00E−53 501 PHE0011615_23861.pep Pkinase 267 523 297.5 2.50E−86 501 PHE0011615_23861.pep Pkinase_Tyr 267 523 127.5 3.70E−35 502 PHE0006925_16814.pep Tim17 4 133 198.1 2.10E−56 503 PHE0006713_16274.pep APC8 1 161 401.5  1.20E−117 503 PHE0006713_16274.pep TPR_1 339 372 34.7 3.20E−07 503 PHE0006713_16274.pep TPR_2 339 372 23.7 0.00066 503 PHE0006713_16274.pep TPR_2 373 406 23.7 0.00068 503 PHE0006713_16274.pep TPR_1 373 406 34.1 4.80E−07 503 PHE0006713_16274.pep TPR_2 407 440 22.1 0.002 503 PHE0006713_16274.pep TPR_1 407 440 24.3 0.00043 504 PHE0008447_18848.pep Lir1 1 126 178.6 1.60E−50 505 PHE0006674_16221.pep PTR2 96 505 222.7 8.20E−64 506 PHE0010613_22398.pep DAGK_cat 43 184 106.4 8.50E−29 507 PHE0002720_22558.pep DnaJ 90 151 137.6 3.40E−38 507 PHE0002720_22558.pep DnaJ_CXXCXGXG 218 301 100.5 5.20E−27 507 PHE0002720_22558.pep DnaJ_C 314 436 210.6 3.60E−60 508 PHE0011760_24005.pep Pkinase 400 656 297.5 2.50E−86 508 PHE0011760_24005.pep Pkinase_Tyr 400 656 127.5 3.70E−35 509 PHE0010612_22397.pep G-patch 15 59 62 1.90E−15 511 PHE0007411_17654.pep Acyltransferase 136 283 86.4 8.50E−23 512 PHE0010617_22402.pep Isochorismatase 27 210 −41 0.0027 513 PHE0010610_22395.pep zf-C3HC4 103 144 36.3 1.10E−07 514 PHE0006883_16702.pep Glyco_transf_5 78 339 461.4  1.10E−135 514 PHE0006883_16702.pep Glycos_transf_1 379 562 40.5 5.80E−09 515 PHE0010636_22408.pep UAA 96 387 −125.2 0.00037 515 PHE0010636_22408.pep DUF6 105 230 32.1 2.00E−06 515 PHE0010636_22408.pep TPT 239 384 188.8 1.30E−53 516 PHE0011082_23038.pep adh_short 19 187 111.5 2.50E−30 516 PHE0011082_23038.pep KR 19 202 −67.5 0.0019 517 PHE0009475_20462.pep 2OG-FeII_Oxy 223 322 166.9 5.20E−47 518 PHE0007415_17661.pep EIN3 60 467 781.6  4.80E−232 519 PHE0006614_16129.pep Cellulase 19 358 −25.9 1.00E−05 520 PHE0010611_22396.pep FMO-like 25 424 −364.7 5.40E−07 521 PHE0011719_23946.pep Acyltransferase 69 222 30 8.30E−06 522 PHE0006861_16463.pep NPH3 166 409 387.6  1.80E−113 523 PHE0006568_16005.pep DUF26 80 134 56.9 6.70E−14 523 PHE0006568_16005.pep DUF26 199 253 62.1 1.80E−15 523 PHE0006568_16005.pep Pkinase_Tyr 346 615 114 4.20E−31 523 PHE0006568_16005.pep Pkinase 346 615 163.2 6.70E−46 524 PHE0010652_22429.pep FtsJ 21 211 282.4 8.80E−82 525 PHE0008158_18448.pep PLATZ 22 144 232.3 1.00E−66 526 PHE0003316_20755.pep Glyco_hydro_2_N 9 180 238.7 1.30E−68 526 PHE0003316_20755.pep Glyco_hydro_2 182 272 129.9 7.00E−36 526 PHE0003316_20755.pep Glyco_hydro_2_C 274 593 612.1  5.00E−181 527 PHE0009478_20470.pep 2OG-FeII_Oxy 229 328 171.2 2.50E−48 528 PHE0010395_21760.pep DUF716 109 266 180.5 4.10E−51 529 PHE0010391_21753.pep DUF640 28 160 296.6 4.70E−86 530 PHE0010396_21761.pep DUF716 109 265 175.2 1.60E−49 531 PHE0009511_22422.pep SAM_decarbox 5 337 710.3  1.30E−210 532 PHE0010614_22399.pep SOUL 28 211 330.7 2.50E−96 534 PHE0011454_23667.pep Histone 56 126 103.3 7.20E−28 535 PHE0011443_24001.pep Histone 61 131 103.3 7.20E−28 536 PHE0011452_23665.pep Histone 58 132 142.7 9.80E−40 537 PHE0010394_21758.pep SAP18 29 150 260.5 3.30E−75 540 PHE0010100_21467.pep Pyr_redox_2 5 285 134.4 3.10E−37 540 PHE0010100_21467.pep Pyr_redox 147 240 91 3.50E−24 540 PHE0010100_21467.pep Fer2_BFD 420 472 81.5 2.60E−21 540 PHE0010100_21467.pep NIR_SIR_ferr 554 621 89.9 7.80E−24 540 PHE0010100_21467.pep NIR_SIR 629 775 176.5 6.70E−50 541 PHE0011503_23734.pep GAF 158 307 91.9 1.90E−24 541 PHE0011503_23734.pep HisKA 343 408 87.5 4.10E−23 541 PHE0011503_23734.pep HATPase_c 455 586 123.9 4.50E−34 542 PHE0010099_21319.pep Molybdop_Fe4S4 1 55 91.2 3.30E−24 542 PHE0010099_21319.pep Molybdopterin 58 475 479.9  3.00E−141 542 PHE0010099_21319.pep Molydop_binding 570 681 140 6.60E−39 542 PHE0010099_21319.pep Fer2_BFD 811 863 74.8 2.70E−19 543 PHE0011269_23400.pep Homeobox 21 78 70.4 5.80E−18 543 PHE0011269_23400.pep START 215 437 167.3 3.90E−47 546 PHE0011613_23858.pep AP2 62 136 129.6 8.70E−36 546 PHE0011613_23858.pep AP2 165 230 109.9 7.50E−30 547 PHE0001582_22064.pep GAF 195 344 57.2 5.30E−14 547 PHE0001582_22064.pep HisKA 380 445 22.2 0.00068 547 PHE0001582_22064.pep Response_reg 645 761 69.4 1.20E−17 548 PHE0007444_22314.pep Spermine_synth 90 349 414.5  1.50E−121 549 PHE0010543_22298.pep PBP 19 165 216.7 5.30E−62 550 PHE0010543_22323.pep PBP 19 157 186 9.30E−53 551 PHE0011081_23033.pep Sugar_tr 33 465 −7.2 1.20E−06 552 PHE0011075_23026.pep P-II 73 175 181.5 2.10E−51 553 PHE0010100_21462.pep Pyr_redox_2 5 285 134.4 3.10E−37 553 PHE0010100_21462.pep Pyr_redox 147 240 91 3.50E−24 553 PHE0010100_21462.pep Fer2_BFD 420 472 81.5 2.60E−21 553 PHE0010100_21462.pep NIR_SIR_ferr 554 621 89.9 7.80E−24 553 PHE0010100_21462.pep NIR_SIR 629 775 176.5 6.70E−50 554 PHE0009640_21775.pep Auxin_inducible 1 102 151.5 2.10E−42 555 PHE0010092_21307.pep S1 13 88 51.4 3.00E−12 555 PHE0010092_21307.pep EIF_2_alpha 125 256 217.3 3.50E−62 556 PHE0004611_24123.pep PTR2 13 406 283.1 5.40E−82 557 PHE0010093_21308.pep S1 13 88 50 8.10E−12 557 PHE0010093_21308.pep EIF_2_alpha 125 256 217.3 3.50E−62 558 PHE0008605_23084.pep Histone 58 128 105.5 1.60E−28 559 PHE0009939_21100.pep GDC-P 81 508 1024.4 0 560 PHE0009941_21105.pep mTERF 2 262 117.5 3.70E−32 561 PHE0009951_21135.pep Ribosomal_L10e 1 176 487.9  1.20E−143 562 PHE0009943_21127.pep Ribosomal_L10e 1 176 460.5  2.20E−135 563 PHE0009948_21132.pep Ribosomal_L10e 1 176 476.4  3.40E−140 564 PHE0011084_23040.pep Peptidase_S10 54 482 561  1.20E−165 565 PHE0008233_23042.pep Phi_1 40 314 616.9  1.80E−182 566 PHE0010854_22730.pep RGS 294 412 23.2 2.80E−06 567 PHE0003797_23051.pep zf-Dof 34 96 127 5.20E−35 568 PHE0010194_21769.pep Glyco_hydro_9 52 509 1007.2  5.70E−300 570 PHE0011665_23899.pep Chloroa_b-bind 63 260 255.3 1.20E−73 571 PHE0012178_24443.pep Whirly 53 191 263.2 5.30E−76 573 PHE0011064_22994.pep TPR_1 73 106 33.7 6.50E−07 573 PHE0011064_22994.pep TPR_2 73 106 33.4 7.80E−07 577 PHE0011446_23659.pep Histone 58 132 142.9 8.50E−40 578 PHE0001424_22077.pep Agglutinin 55 193 46.9 6.30E−12 579 PHE0011445_23658.pep C2 6 87 74.9 2.50E−19 580 PHE0010090_21297.pep LRRNT_2 33 73 34.2 4.60E−07 580 PHE0010090_21297.pep LRR_1 78 101 11.5 2 580 PHE0010090_21297.pep LRR_1 103 127 11.2 2.3 580 PHE0010090_21297.pep LRR_1 129 151 21.9 0.0024 580 PHE0010090_21297.pep LRR_1 177 199 16 0.14 580 PHE0010090_21297.pep LRR_1 226 248 10.3 3.3 580 PHE0010090_21297.pep LRR_1 274 296 18.9 0.018 580 PHE0010090_21297.pep LRR_1 298 320 12.1 1.6 580 PHE0010090_21297.pep LRR_1 322 341 11.2 2.3 580 PHE0010090_21297.pep LRR_1 395 417 9.8 4.1 580 PHE0010090_21297.pep LRR_1 444 466 8.2 8.3 580 PHE0010090_21297.pep LRR_1 468 490 12.8 1.1 580 PHE0010090_21297.pep LRR_1 492 514 7.7 10 580 PHE0010090_21297.pep LRR_1 516 538 15.7 0.17 580 PHE0010090_21297.pep LRR_1 540 562 7.8 10 580 PHE0010090_21297.pep LRR_1 564 585 8.5 7.4 580 PHE0010090_21297.pep Pkinase 678 952 107.9 3.00E−29 580 PHE0010090_21297.pep Pkinase_Tyr 678 952 110.4 5.10E−30 581 PHE0012180_24445.pep B3 516 619 90.3 6.00E−24 582 PHE0011083_23039.pep adh_short 44 200 46.7 7.60E−11 583 PHE0011085_23041.pep Peptidase_S10 31 459 551.6  8.20E−163 584 PHE0012175_24440.pep CXC 457 498 80.2 6.60E−21 584 PHE0012175_24440.pep CXC 543 584 83.5 6.40E−22 585 PHE0012177_24442.pep Whirly 91 229 325.2 1.10E−94 587 PHE0010194_21426.pep Glyco_hydro_9 52 509 1013.8  5.70E−302 588 PHE0011666_23900.pep Spermine_synth 46 291 503.1  3.20E−148 589 PHE0011448_24160.pep Histone 25 90 35.4 1.90E−07 590 PHE0008324_18636.pep DUF1005 256 460 524.8  9.30E−155 591 PHE0006971_16875.pep Myb_DNA-binding 14 61 44.2 4.40E−10 591 PHE0006971_16875.pep Myb_DNA-binding 67 112 51.3 3.20E−12 592 PHE0009939_21147.pep GDC-P 81 508 1024.4 0 593 PHE0009953_21137.pep Na_sulph_symp 110 578 831.2  5.40E−247 595 PHE0008557_18970.pep NAD_binding_1 234 350 138.6 1.60E−38 596 PHE0006443_15955.pep YDG_SRA 360 519 403.5  3.00E−118 596 PHE0006443_15955.pep Pre-SET 543 639 156.7 6.00E−44 596 PHE0006443_15955.pep SET 641 771 181.7 1.80E−51

TABLE 11 pfam module annotation PEP SEQ ID NO Gene ID Pfam domain module Position 299 PHE0007721_18998.pep KNOX1::KNOX2::ELK 102-146::153-204::242-263 300 PHE0007756_18009.pep RPE65 105-591 302 PHE0004988_15925.pep F-box::LRR_1::LRR_2 4-52::157-179::290-314 303 PHE0007140_21771.pep MtN3_slv::MtN3_slv 9-98::134-221 304 PHE0006823_16403.pep Globin 10-149 305 PHE0007440_22555.pep Ras 14-175 306 PHE0000206_22432.pep Pkinase::efhand::efhand:: 79-337::384-412::456- efhand 484::490-518 307 PHE0000598_16824.pep HLH 385-434 308 PHE0007590_17883.pep S1 2-70 309 PHE0007588_17881.pep S1 2-86 310 PHE0007592_17885.pep S1 1-75 311 PHE0007587_17880.pep S1 3-75 312 PHE0007624_17923.pep eIF-1a 5-70 313 PHE0007591_17884.pep S1 2-68 314 PHE0007623_17922.pep CN_hydrolase 11-184 315 PHE0007583_17871.pep MtN3_slv::MtN3_slv 9-98::132-218 316 PHE0006618_16146.pep S10_plectin 3-98 317 PHE0006791_16374.pep GUN4 84-227 318 PHE0007620_17918.pep peroxidase 89-321 319 PHE0006659_16195.pep MFS_1 10-391 321 PHE0006274_15867.pep E2F_TDP 130-195 322 PHE0006637_16166.pep PP2C 7-305 323 PHE0006926_16815.pep VPS28 18-209 324 PHE0006821_16402.pep PALP 49-358 325 PHE0007687_18057.pep p450 35-462 326 PHE0007642_17999.pep PAS_3::PAS_3::Pkinase 211-303::489-581::663-952 327 PHE0007677_18052.pep FAD_binding_3 5-372 328 PHE0007644_18001.pep LRRNT_2::LRR_1::LRR_1:: 23-64::97-119::121-143::145- LRR_1::LRR_1::LRR_1:: 167::169-192::194-216::414-716 Pkinase 329 PHE0007640_17992.pep CorA 66-448 330 PHE0007678_18053.pep 4HBT 66-151 331 PHE0007649_18006.pep Ank::Pkinase 108-140::196-455 332 PHE0006726_16298.pep WD40::WD40 45-83::135-173 333 PHE0006218_8776.pep Pyr_redox_2::Thioredoxin 85-370::423-528 335 PHE0002554_17876.pep Chloroa_b-bind 63-261 336 PHE0006807_16388.pep CCT 352-390 337 PHE0003359_8487.pep p450 51-489 338 PHE0006542_15765.pep PMSR 92-245 339 PHE0007622_17921.pep Spermine_synth 34-279 340 PHE0007630_17956.pep 2OG-FeII_Oxy 190-291 341 PHE0007593_17886.pep Spermine_synth 28-273 342 PHE0006475_15588.pep PsbQ 3-162 343 PHE0007619_17915.pep MBD 11-84 344 PHE0006846_16447.pep Sterol_desat 1-186 345 PHE0007584_17874.pep MBD 4-77 346 PHE0003695_17913.pep LRRNT_2::LRR_1::LRR_1:: 23-64::93-115::117-139::141- LRR_1::LRR_1::LRR_1:: 163::165-186::189-211::213- LRR_1::LRR_1::LRR_1:: 235::237-259::260-281::284- LRR_1::LRR_1::LRR_1:: 306::308-330::332-354::356- LRR_1::LRR_1::LRR_1:: 378::380-402::404-426::428- LRR_1::LRR_1::LRR_1:: 450::452-474::476-498::500- LRR_1::LRR_1::Pkinase 521::523-542::648-917 347 PHE0003695_17879.pep LRRNT_2::LRR_1::LRR_1:: 23-64::93-115::117-139::141- LRR_1::LRR_1::LRR_1:: 163::165-186::189-211::213- LRR_1::LRR_1::LRR_1:: 235::237-259::260-281::284- LRR_1::LRR_1::LRR_1:: 306::308-330::332-354::356- LRR_1::LRR_1::LRR_1:: 378::380-402::404-426::428- LRR_1::LRR_1::LRR_1:: 450::452-474::476-498::500- LRR_1::LRR_1::Pkinase 521::523-542::648-917 349 PHE0007645_18002.pep AP2 115-180 350 PHE0006784_16366.pep PALP 12-301 351 PHE0006171_16491.pep Glyoxalase 70-214 353 PHE0006906_16796.pep Proteasome 10-206 354 PHE0006649_16180.pep AP2 46-110 355 PHE0006809_16390.pep Prismane 1-548 356 PHE0006918_16808.pep SWIM 321-353 357 PHE0007813_18219.pep MtN3_slv::MtN3_slv 9-98::132-218 359 PHE0006825_16405.pep Cytochrom_C552 27-476 360 PHE0006964_16864.pep tRNA_anti::tRNA-synt_2 43-122::140-557 361 PHE0008105_18407.pep CBFD_NFYB_HMF 158-222 362 PHE0006630_16159.pep Ldh_1_N::Ldh_1_C 90-239::241-413 363 PHE0006966_16868.pep DNA_photolyase:: 12-183::214-492 FAD_binding_7 365 PHE0006608_16123.pep GSHPx 42-150 366 PHE0010462_21459.pep NUDIX::NUDIX 17-159::190-322 367 PHE0009211_21774.pep Auxin_inducible 1-106 368 PHE0006256_8775.pep RPE65 105-591 369 PHE0006989_16918.pep Pkinase 88-396 370 PHE0007649_18166.pep Ank::Pkinase 108-140::196-455 371 PHE0006708_16264.pep DEAD::Helicase_C 57-223::291-367 372 PHE0001117_19094.pep Homeobox::HALZ 79-133::134-178 373 PHE0006266_8814.pep Fe_bilin_red 16-244 374 PHE0006795_16378.pep Na_H_antiport_1 4-380 375 PHE0006956_16853.pep Molybdop_Fe4S4:: 2-56::59-482::578-689::825- Molybdopterin:: 877 Molydop_binding:: Fer2_BFD 377 PHE0006824_16404.pep Globin 14-154 378 PHE0006812_16393.pep Bac_globin 3-118 379 PHE0006815_16396.pep Bac_globin 26-146 380 PHE0006806_16387.pep Bac_globin 26-146 381 PHE0006624_16153.pep NAD_binding_2::6PGD 3-178::182-473 382 PHE0005006_15823.pep Chloroa_b-bind 63-242 384 PHE0006683_16229.pep Response_reg 10-151 385 PHE0006884_16703.pep Glyco_transf_5:: 83-344::384-567 Glycos_transf_1 386 PHE0006691_16237.pep NAD_Gly3P_dh_N:: 6-165::183-327 NAD_Gly3P_dh_C 387 PHE0006790_16372.pep Rieske::PaO 220-317::408-507 388 PHE0009143_19932.pep Histone_HNS 21-129 389 PHE0008406_18830.pep AA_permease 57-511 390 PHE0008279_18708.pep Mit_rib_S27 14-93 391 PHE0009142_19931.pep Histone_HNS 21-130 393 PHE0007639_17991.pep ELFV_dehydrog_N:: 84-214::229-474 ELFV_dehydrog 394 PHE0007646_18170.pep F-box::Kelch_1:: 36-83::131-185::187-233 Kelch_1 395 PHE0007765_18182.pep GST_N::GST_C 5-79::101-204 396 PHE0008167_18465.pep Pkinase_Tyr 8-262 398 PHE0008183_18479.pep LRRNT_2::LRR_1::LRR_1:: 23-66::71-93::95-117::119- LRR_1::LRR_1::LRR_1:: 142::144-166::168-190::192- LRR_1::LRR_1::LRR_1:: 214::289-311::313-335::337- LRR_1::LRR_1::LRR_1:: 359::361-384::409-431::457- LRR_1::LRR_1::LRR_1:: 479::481-503::505-527::529- LRR_1::LRR_1::LRR_1:: 551::553-575::577-598::695- Pkinase_Tyr 966 399 PHE0007585_17875.pep LEA_3 35827 400 PHE0006804_16385.pep zf-CCCH::zf-CCCH 13-39::149-174 401 PHE0006703_15751.pep PFK 72-347 402 PHE0007410_17653.pep Acyltransferase 27-249 403 PHE0006854_16456.pep YABBY 40-278 404 PHE0007721_21293.pep KNOX1::KNOX2::ELK 102-146::153-204::242-263 405 PHE0006563_15990.pep GATase_2::Asn_synthase 2-161::209-450 406 PHE0006619_16147.pep AA_kinase 15-261 407 PHE0006813_16394.pep Bac_globin 7-124 408 PHE0006688_16234.pep Ribosomal_S2 13-229 409 PHE0006635_16164.pep MGS 28-121 411 PHE0008416_18838.pep PTR2 115-504 413 PHE0008599_19166.pep Isoamylase_N::Alpha- 24-115::164-578 amylase 414 PHE0008375_18732.pep Pribosyltran 93-237 416 PHE0008394_18763.pep Gln-synt_N::Gln-synt_C 68-148::154-406 417 PHE0008395_18764.pep Gln-synt_N::Gln-synt_C 68-148::154-406 418 PHE0008444_18846.pep Gln-synt_N::Gln-synt_C 17-97::103-355 419 PHE0006819_16400.pep Lactamase_B::Flavodoxin_1:: 47-236::267-397::424-573 Flavin_Reduct 420 PHE0007417_17663.pep EIN3 60-467 421 PHE0008443_18845.pep GATase_2::Asn_synthase 2-161::209-450 422 PHE0006818_16399.pep Lactamase_B::Flavodoxin_1:: 34-227::256-389::423-471 Rubredoxin 423 PHE0006579_16031.pep Thi4 63-306 424 PHE0006808_16389.pep CCT 354-392 425 PHE0008160_18460.pep TPP_enzyme_N:: 45-221::243-376::431-578 TPP_enzyme_M:: TPP_enzyme_C 426 PHE0007571_17834.pep GSH_synth_ATP 29-499 427 PHE0007586_17877.pep Chloroa_b-bind 64-261 429 PHE0009729_21717.pep Homeobox::HALZ 67-123::124-168 430 PHE0006424_15520.pep PsbW_2 1-133 431 PHE0006392_15480.pep PsbP 106-322 432 PHE0006589_16093.pep Thioredoxin 64-167 433 PHE0009258_21487.pep Na_H_Exchanger 22-441 434 PHE0006680_16226.pep 2OG-FeII_Oxy 187-287 435 PHE0006481_16072.pep adh_short 33-181 436 PHE0006269_8820.pep TPR_2::TPR_1::TPR_2:: 74-107::108-141::142- TPR_1::TPR_4::TPR_2:: 175::179-212::247-272::281- TPR_1 314::349-382 437 PHE0006783_16365.pep Aa_trans 32-469 438 PHE0003151_18392.pep AP2::AP2 318-391::420-485 439 PHE0008272_18723.pep HSF_DNA-bind 18-188 440 PHE0008277_18706.pep SNF5 172-400 441 PHE0008109_18411.pep Sad1_UNC 203-330 442 PHE0008280_18826.pep Alpha-amylase 14-452 443 PHE0002424_15825.pep adh_short 43-215 444 PHE0006914_16804.pep AAA 204-391 445 PHE0006642_16172.pep p450 42-496 447 PHE0009926_21079.pep DSPc 24-152 448 PHE0006206_19159.pep Sina 106-305 449 PHE0008274_18705.pep BURP 56-280 450 PHE0009510_20526.pep Spermine_synth 38-283 451 PHE0009937_21097.pep Spermine_synth 38-283 452 PHE0009927_21080.pep DSPc 24-162 454 PHE0006445_15956.pep Allene_ox_cyc 74-253 455 PHE0006987_16893.pep efhand::efhand 86-114::167-195 456 PHE0004230_15865.pep E2F_TDP 146-211 457 PHE0006814_16395.pep Bac_globin 26-144 458 PHE0002773_15881.pep NTP_transferase 88-366 459 PHE0006060_15842.pep ubiquitin::ubiquitin:: 5-73::81-149::157-225::233- ubiquitin::ubiquitin 301 460 PHE0006850_16451.pep YABBY 6-166 461 PHE0008043_18199.pep Homeobox::START:: 25-85::164-374::693-840 MEKHLA 462 PHE0000125_18852.pep Response_reg::CCT 28-153::457-495 463 PHE0008269_18720.pep Pkinase 23-279 464 PHE0008264_18712.pep zf-UBR 40-109 465 PHE0002782_20059.pep PGI 2-457 466 PHE0009438_20404.pep GATA 191-226 467 PHE0009429_20392.pep ParBc 70-151 468 PHE0009440_20406.pep ParBc 11-126 469 PHE0008543_18945.pep TP_methylase 222-435 470 PHE0006960_16857.pep Oxidored_molyb:: 116-301::326-459::515- Mo-co_dimer::Cyt- 588::633-740::759-872 b5::FAD_binding_6:: NAD_binding_1 471 PHE0009427_20389.pep IGPD 103-247 472 PHE0006437_15906.pep Pkinase 39-307 473 PHE0007409_17652.pep DAGAT 64-340 474 PHE0009426_20387.pep PHP 2-281 475 PHE0009430_20393.pep ParBc 44-128 476 PHE0007003_16906.pep PTPA 96-396 477 PHE0008378_18741.pep bZIP_1 223-280 478 PHE0008273_18725.pep zf-CCCH 80-106 479 PHE0008547_18953.pep Fer2 20-95 480 PHE0006922_16812.pep Hexokinase_1:: 44-251::258-501 Hexokinase_2 481 PHE0006920_16810.pep AAA::Vps4_C 267-458::464-514 482 PHE0008396_18765.pep Gln-synt_N::Gln-synt_C 68-148::154-406 483 PHE0006957_16854.pep Gln-synt_N::Gln-synt_C 68-148::154-406 484 PHE0006404_15936.pep RRM_1::RRM_1 8-77::112-182 485 PHE0006820_16401.pep Lactamase_B::Flavin_Reduct 47-236::423-572 486 PHE0006690_16236.pep MFS_1 57-421 487 PHE0006395_15932.pep LRR_1::LRR_1::LRR_1:: 185-206::208-229::231- LRR_1::LRR_1::LRR_1:: 252::254-272::278-299::349- LRR_1 370::372-394 488 PHE0006759_16384.pep SHMT 55-453 489 PHE0006576_16028.pep Myb_DNA-binding:: 11-57::63-108 Myb_DNA-binding 490 PHE0006979_16885.pep Tryp_alpha_amyl 33-111 491 PHE0009786_21754.pep HLH 33-80 492 PHE0006572_16007.pep Pkinase 11-269 494 PHE0006588_16092.pep Thioredoxin 56-161 495 PHE0006985_16891.pep DUF1716 13-118 496 PHE0006875_16688.pep PSI_PSAK 44-138 497 PHE0006626_16155.pep Glyco_hydro_17 30-335 498 PHE0006689_16235.pep Aa_trans 165-548 499 PHE0006799_16382.pep B12-binding:: 10-135::202-368 Radical_SAM 500 PHE0006959_16856.pep Oxidored_molyb:: 143-328::353-486::543- Mo-co_dimer::Cyt-b5:: 616::660-767::786-899 FAD_binding_6:: NAD_binding_1 501 PHE0011615_23861.pep Pkinase 267-523 502 PHE0006925_16814.pep Tim17 4-133 503 PHE0006713_16274.pep APC8::TPR_1::TPR_1:: l-161::339-372::373- TPR_1 406::407-440 504 PHE0008447_18848.pep Lir1 1-126 505 PHE0006674_16221.pep PTR2 96-505 506 PHE0010613_22398.pep DAGK_cat 43-184 507 PHE0002720_22558.pep DnaJ::DnaJ_CXXCXGXG:: 90-151::218-301::314-436 DnaJ_C 508 PHE0011760_24005.pep Pkinase 400-656 509 PHE0010612_22397.pep G-patch 15-59 511 PHE0007411_17654.pep Acyltransferase 136-283 512 PHE0010617_22402.pep Isochorismatase 27-210 513 PHE0010610_22395.pep zf-C3HC4 103-144 514 PHE0006883_16702.pep Glyco_transf_5:: 78-339::379-562 Glycos_transf_1 515 PHE0010636_22408.pep DUF6::TPT 105-230::239-384 516 PHE0011082_23038.pep adh_short 19-187 517 PHE0009475_20462.pep 2OG-FeII_Oxy 223-322 518 PHE0007415_17661.pep EIN3 60-467 519 PHE0006614_16129.pep Cellulase 19-358 520 PHE0010611_22396.pep FMO-like 25-424 521 PHE0011719_23946.pep Acyltransferase 69-222 522 PHE0006861_16463.pep NPH3 166-409 523 PHE0006568_16005.pep DUF26::DUF26::Pkinase 80-134::199-253::346-615 524 PHE0010652_22429.pep FtsJ 21-211 525 PHE0008158_18448.pep PLATZ 22-144 526 PHE0003316_20755.pep Glyco_hydro_2_N:: 9-180::182-272::274-593 Glyco_hydro_2:: Glyco_hydro_2_C 527 PHE0009478_20470.pep 2OG-FeII_Oxy 229-328 528 PHE0010395_21760.pep DUF716 109-266 529 PHE0010391_21753.pep DUF640 28-160 530 PHE0010396_21761.pep DUF716 109-265 531 PHE0009511_22422.pep SAM_decarbox 5-337 532 PHE0010614_22399.pep SOUL 28-211 534 PHE0011454_23667.pep Histone 56-126 535 PHE0011443_24001.pep Histone 61-131 536 PHE0011452_23665.pep Histone 58-132 537 PHE0010394_21758.pep SAP18 29-150 540 PHE0010100_21467.pep Pyr_redox_2::Fer2_BFD:: 5-285::420-472::554- NIR_SIR_ferr::NIR_SIR 621::629-775 541 PHE0011503_23734.pep GAF::HisKA::HATPase_c 158-307::343-408::455-586 542 PHE0010099_21319.pep Molybdop_Fe4S4:: 1-55::58-475::570-681::811- Molybdopterin:: 863 Molydop_binding:: Fer2_BFD 543 PHE0011269_23400.pep Homeobox::START 21-78::215-437 546 PHE0011613_23858.pep AP2::AP2 62-136::165-230 547 PHE0001582_22064.pep GAF::HisKA::Response_reg 195-344::380-445::645-761 548 PHE0007444_22314.pep Spermine_synth 90-349 549 PHE0010543_22298.pep PBP 19-165 550 PHE0010543_22323.pep PBP 19-157 551 PHE0011081_23033.pep Sugar_tr 33-465 552 PHE0011075_23026.pep P-II 73-175 553 PHE0010100_21462.pep Pyr_redox_2::Fer2_BFD:: 5-285::420-472::554- NIR_SIR_ferr::NIR_SIR 621::629-775 554 PHE0009640_21775.pep Auxin_inducible 1-102 555 PHE0010092_21307.pep S1::EIF_2_alpha 13-88::125-256 556 PHE0004611_24123.pep PTR2 13-406 557 PHE0010093_21308.pep S1::EIF_2_alpha 13-88::125-256 558 PHE0008605_23084.pep Histone 58-128 559 PHE0009939_21100.pep GDC-P 81-508 560 PHE0009941_21105.pep mTERF 2-262 561 PHE0009951_21135.pep Ribosomal_L10e 1-176 562 PHE0009943_21127.pep Ribosomal_L10e 1-176 563 PHE0009948_21132.pep Ribosomal_L10e 1-176 564 PHE0011084_23040.pep Peptidase_S10 54-482 565 PHE0008233_23042.pep Phi_1 40-314 566 PHE0010854_22730.pep RGS 294-412 567 PHE0003797_23051.pep zf-Dof 34-96 568 PHE0010194_21769.pep Glyco_hydro_9 52-509 570 PHE0011665_23899.pep Chloroa_b-bind 63-260 571 PHE0012178_24443.pep Whirly 53-191 573 PHE0011064_22994.pep TPR_1 73-106 577 PHE0011446_23659.pep Histone 58-132 578 PHE0001424_22077.pep Agglutinin 55-193 579 PHE0011445_23658.pep C2 6-87 580 PHE0010090_21297.pep LRRNT_2::LRR_1::LRR_1:: 33-73::78-101::103-127::129- LRR_1::LRR_1::LRR_1:: 151::177-199::226-248::274- LRR_1::LRR_1::LRR_1:: 296::298-320::322-341::395- LRR_1::LRR_1::LRR_1:: 417::444-466::468-490::492- LRR_1::LRR_1::LRR_1:: 514::516-538::540-562::564- LRR_1::Pkinase_Tyr 585::678-952 581 PHE0012180_24445.pep B3 516-619 582 PHE0011083_23039.pep adh_short 44-200 583 PHE0011085_23041.pep Peptidase_S10 31-459 584 PHE0012175_24440.pep CXC::CXC 457-498::543-584 585 PHE0012177_24442.pep Whirly 91-229 587 PHE0010194_21426.pep Glyco_hydro_9 52-509 588 PHE0011666_23900.pep Spermine_synth 46-291 589 PHE0011448_24160.pep Histone 25-90 590 PHE0008324_18636.pep DUF1005 256-460 591 PHE0006971_16875.pep Myb_DNA-binding:: 14-61::67-112 Myb_DNA-binding 592 PHE0009939_21147.pep GDC-P 81-508 593 PHE0009953_21137.pep Na_sulph_symp 110-578 595 PHE0008557_18970.pep NAD_binding_1 234-350 596 PHE0006443_15955.pep YDG_SRA::Pre- 360-519::543-639::641-771 SET::SET

TABLE 12 Description of pfam domains Accession Gathering Pfam domain name number cutoff Domain description 2OG-FeII_Oxy PF03171.10 11.5 2OG-Fe(II) oxygenase superfamily 4HBT PF03061.12 20.6 Thioesterase superfamily 6PGD PF00393.9 −232.3 6-phosphogluconate dehydrogenase, C-terminal domain AAA PF00004.19 12.3 ATPase family associated with various cellular activities (AAA) AA_kinase PF00696.18 −40 Amino acid kinase family AA_permease PF00324.11 −120.8 Amino acid permease AP2 PF00847.10 0 AP2 domain APC8 PF04049.4 −19.8 Anaphase promoting complex subunit 8/ Cdc23 Aa_trans PF01490.8 −128.4 Transmembrane amino acid transporter protein Acyltransferase PF01553.11 −0.4 Acyltransferase Agglutinin PF07468.2 25 Agglutinin Allene_ox_cyc PF06351.2 25 Allene oxide cyclase Alpha-amylase PF00128.14 −92.6 Alpha amylase, catalytic domain Ank PF00023.20 0 Ankyrin repeat ApbA PF02558.6 −16.2 Ketopantoate reductase PanE/ApbA Asn_synthase PF00733.11 −52.8 Asparagine synthase Auxin_inducible PF02519.5 −15 Auxin responsive protein B12-binding PF02310.9 19.6 B12 binding domain B3 PF02362.12 26.5 B3 DNA binding domain BURP PF03181.6 −52 BURP domain Bac_globin PF01152.11 −12.7 Bacterial-like globin C2 PF00168.20 3.7 C2 domain CBFD_NFYB_HMF PF00808.13 18.4 Histone-like transcription factor (CBF/NF-Y) and archaeal histone CCT PF06203.4 25 CCT motif CN_hydrolase PF00795.12 −13.9 Carbon-nitrogen hydrolase CXC PF03638.5 25 Tesmin/TSO1-like CXC domain Cellulase PF00150.8 −49.3 Cellulase (glycosyl hydrolase family 5) Chloroa_b-bind PF00504.12 −31.9 Chlorophyll A-B binding protein CorA PF01544.9 −61.3 CorA-like Mg2+ transporter protein Cyt-b5 PF00173.18 4 Cytochrome b5-like Heme/Steroid binding domain Cytochrom_C552 PF02335.6 −166 Cytochrome c552 DAGAT PF03982.3 −151.7 Diacylglycerol acyltransferase DAGK cat PF00781.14 −5.7 Diacylglycerol kinase catalytic domain (presumed) DAO PF01266.14 −35 FAD dependent oxidoreductase DEAD PF00270.19 7.2 DEAD/DEAH box helicase DNA_photolyase PF00875.8 26.1 DNA photolyase DSPc PF00782.11 −21.8 Dual specificity phosphatase, catalytic domain DUF1005 PF06219.3 25 Protein of unknown function (DUF1005) DUF1716 PF08216.2 25 Eukaryotic domain of unknown function (DUF1716) DUF26 PF01657.8 0 Domain of unknown function DUF26 DUF6 PF00892.11 20.8 Integral membrane protein DUF6 DUF640 PF04852.3 2.4 Protein of unknown function (DUF640) DUF716 PF04819.3 −18.4 Family of unknown function (DUF716) DnaJ PF00226.21 −8 DnaJ domain DnaJ_C PF01556.9 −24 DnaJ C terminal region DnaJ_CXXCXGXG PF00684.9 1 DnaJ central domain (4 repeats) E2F_TDP PF02319.11 17 E2F/DP family winged-helix DNA- binding domain EIF_2_alpha PF07541.2 −4.2 Eukaryotic translation initiation factor 2 alpha subunit EIN3 PF04873.4 −137.6 Ethylene insensitive 3 ELFV_dehydrog PF00208.11 −27 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ELFV_dehydrog_N PF02812.8 31.8 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain ELK PF03789.4 25 ELK domain F-box PF00646.23 13.9 F-box domain FAD_binding_3 PF01494.9 −136.6 FAD binding domain FAD_binding_6 PF00970.14 −11.4 Oxidoreductase FAD-binding domain FAD_binding_7 PF03441.4 25 FAD binding domain of DNA photolyase FMO-like PF00743.9 −381.6 Flavin-binding monooxygenase-like Fe_bilin_red PF05996.3 25 Ferredoxin-dependent bilin reductase Fer2 PF00111.17 7 2Fe—2S iron-sulfur cluster binding domain Fer2_BFD PF04324.5 25 BFD-like [2Fe—2S] binding domain Flavin_Reduct PF01613.8 −18 Flavin reductase like domain Flavodoxin_1 PF00258.15 6.3 Flavodoxin FtsJ PF01728.9 −50.2 FtsJ-like methyltransferase G-patch PF01585.13 18.3 G-patch domain GAF PF01590.16 23 GAF domain GATA PF00320.17 28.5 GATA zinc finger GATase_2 PF00310.11 −95.1 Glutamine amidotransferases class-II GDC-P PF02347.6 −306.2 Glycine cleavage system P-protein GSHPx PF00255.10 −16 Glutathione peroxidase GSH_synth_ATP PF03917.8 −129.9 Eukaryotic glutathione synthase, ATP binding domain GSH_synthase PF03199.6 25 Eukaryotic glutathione synthase GST_C PF00043.15 22.3 Glutathione S-transferase, C-terminal domain GST_N PF02798.10 14.6 Glutathione S-transferase, N-terminal domain GUN4 PF05419.3 25 GUN4-like Gln-synt_C PF00120.14 −124 Glutamine synthetase, catalytic domain Gln-synt_N PF03951.9 9 Glutamine synthetase, beta-Grasp domain Globin PF00042.12 −8.8 Globin Glutaredoxin PF00462.14 17.2 Glutaredoxin Glyco_hydro_17 PF00332.9 −152.3 Glycosyl hydrolases family 17 Glyco_hydro_2 PF00703.11 −19.3 Glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich domain Glyco_hydro_2_C PF02836.7 −127.7 Glycosyl hydrolases family 2, TIM barrel domain Glyco_hydro_2_N PF02837.8 −46.9 Glycosyl hydrolases family 2, sugar binding domain Glyco_hydro_9 PF00759.9 −246.7 Glycosyl hydrolase family 9 Glyco_transf_5 PF08323.2 −114.9 Starch synthase catalytic domain Glycos_transf_1 PF00534.10 −7.3 Glycosyl transferases group 1 Glyoxalase PF00903.15 12.1 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily HALZ PF02183.8 17 Homeobox associated leucine zipper HATPase_c PF02518.16 22.4 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase HLH PF00010.16 8.3 Helix-loop-helix DNA-binding domain HSF_DNA-bind PF00447.8 −70 HSF-type DNA-binding Helicase_C PF00271.21 2.1 Helicase conserved C-terminal domain Hexokinase_1 PF00349.11 −110.3 Hexokinase Hexokinase_2 PF03727.6 −131.3 Hexokinase HisKA PF00512.15 10.3 His Kinase A (phosphoacceptor) domain Histone PF00125.14 17.4 Core histone H2A/H2B/H3/H4 Histone_HNS PF00816.11 25 H-NS histone family Homeobox PF00046.19 −4.1 Homeobox domain IGPD PF00475.9 25 Imidazoleglycerol-phosphate dehydratase Isoamylase_N PF02922.8 −6.5 Isoamylase N-terminal domain Isochorismatase PF00857.11 −46 Isochorismatase family KNOX1 PF03790.4 25 KNOX1 domain KNOX2 PF03791.4 25 KNOX2 domain KR PF08659.1 −74.3 KR domain Kelch_1 PF01344.15 7.8 Kelch motif Kelch_2 PF07646.5 14 Kelch motif LEA_3 PF03242.4 25 Late embryogenesis abundant protein LRRNT_2 PF08263.3 18.6 Leucine rich repeat N-terminal domain LRR_1 PF00560.23 7.7 Leucine Rich Repeat LRR_2 PF07723.3 6 Leucine Rich Repeat Lactamase_B PF00753.17 24.6 Metallo-beta-lactamase superfamily Ldh_1_C PF02866.8 −13 lactate/malate dehydrogenase, alpha/beta C-terminal domain Ldh_1_N PF00056.13 −31.3 lactate/malate dehydrogenase, NAD binding domain Lir1 PF07207.2 25 Light regulated protein Lir1 MBD PF01429.10 12.9 Methyl-CpG binding domain MEKHLA PF08670.1 −59.7 MEKHLA domain MFS_1 PF07690.6 23.5 Major Facilitator Superfamily MGS PF02142.12 3 MGS-like domain Miro PF08477.3 10.8 Miro-like protein Mit_rib_S27 PF08293.2 25 Mitochondrial ribosomal subunit S27 Mo-co_dimer PF03404.6 25 Mo-co oxidoreductase dimerisation domain Molybdop_Fe4S4 PF04879.6 13.6 Molybdopterin oxidoreductase Fe4S4 domain Molybdopterin PF00384.12 −50 Molybdopterin oxidoreductase Molydop_binding PF01568.11 1.1 Molydopterin dinucleotide binding domain MtN3_slv PF03083.6 9.7 MtN3/saliva family Myb_DNA-binding PF00249.21 14 Myb-like DNA-binding domain NAD_Gly3P_dh_C PF07479.4 −50.8 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus NAD_Gly3P_dh_N PF01210.13 −44 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus NAD_binding_1 PF00175.11 −3.9 Oxidoreductase NAD-binding domain NAD_binding_2 PF03446.5 −63.5 NAD binding domain of 6- phosphogluconate dehydrogenase NIR_SIR PF01077.12 −19.6 Nitrite and sulphite reductase 4Fe—4S domain NIR_SIR_ferr PF03460.7 2.4 Nitrite/Sulfite reductase ferredoxin-like half domain NPH3 PF03000.5 25 NPH3 family NTP_transferase PF00483.13 −90.5 Nucleotidyl transferase NUDIX PF00293.18 0.2 NUDIX domain Na_H_Exchanger PF00999.11 −67.9 Sodium/hydrogen exchanger family Na_H_antiport_1 PF06965.2 −270.8 Na+/H+ antiporter 1 Na_sulph_symp PF00939.9 −259 Sodium:sulfate symporter transmembrane region Oxidored_molyb PF00174.9 −39.6 Oxidoreductase molybdopterin binding domain P-II PF00543.12 −29 Nitrogen regulatory protein P-II PALP PF00291.15 −70 Pyridoxal-phosphate dependent enzyme PAS PF00989.14 0 PAS fold PAS_3 PF08447.1 13.4 PAS fold PBP PF01161.10 −20.6 Phosphatidylethanolamine-binding protein PFK PF00365.10 −132 Phosphofructokinase PGI PF00342.9 −168.9 Phosphoglucose isomerase PHP PF02811.9 13.8 PHP domain PLATZ PF04640.4 20 PLATZ transcription factor PMSR PF01625.11 −62 Peptide methionine sulfoxide reductase PP2C PF00481.12 −44 Protein phosphatase 2C PSI_PSAK PF01241.9 25 Photosystem I psaG/psaK PTPA PF03095.5 −106 Phosphotyrosyl phosphate activator (PTPA) protein PTR2 PF00854.12 −50 POT family PaO PF08417.2 25 Pheophorbide a oxygenase ParBc PF02195.8 25 ParB-like nuclease domain Peptidase_S10 PF00450.12 −198 Serine carboxypeptidase Phi_1 PF04674.3 25 Phosphate-induced protein 1 conserved region Pkinase PF00069.15 −70.3 Protein kinase domain Pkinase_Tyr PF07714.7 65 Protein tyrosine kinase Pre-SET PF05033.6 3.9 Pre-SET motif Pribosyltran PF00156.17 2 Phosphoribosyl transferase domain Prismane PF03063.10 −169.3 Prismane/CO dehydrogenase family Proteasome PF00227.16 −36.7 Proteasome A-type and B-type PsbP PF01789.7 25 PsbP PsbQ PF05757.2 25 Oxygen evolving enhancer protein 3 (PsbQ) PsbW_2 PF07123.2 −25.8 Photosystem II reaction centre W protein (PsbW) Pyr_redox PF00070.17 5 Pyridine nucleotide-disulphide oxidoreductase Pyr_redox_2 PF07992.4 −20 Pyridine nucleotide-disulphide oxidoreductase RGS PF00615.9 10 Regulator of G protein signaling domain RPE65 PF03055.6 −156.5 Retinal pigment epithelial membrane protein RRM_1 PF00076.12 17.7 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) Radical_SAM PF04055.11 8.5 Radical SAM superfamily Ras PF00071.12 −69.9 Ras family Response_reg PF00072.14 4 Response regulator receiver domain Ribosomal_L10e PF00826.8 25 Ribosomal L10 Ribosomal_S2 PF00318.10 −22 Ribosomal protein S2 Rieske PF00355.16 −7 Rieske [2Fe—2S] domain Rubredoxin PF00301.10 12.1 Rubredoxin S1 PF00575.13 16.8 S1 RNA binding domain S10_plectin PF03501.5 25 Plectin/S10 domain SAM_decarbox PF01536.7 −154 Adenosylmethionine decarboxylase SAP18 PF06487.3 −49.7 Sin3 associated polypeptide p18 (SAP18) SET PF00856.18 23.5 SET domain SHMT PF00464.10 −238.5 Serine hydroxymethyltransferase SNF5 PF04855.3 25 SNF5/SMARCB1/INI1 SOUL PF04832.3 25 SOUL heme-binding protein START PF01852.10 −20.7 START domain SWIM PF04434.8 11 SWIM zinc finger Sad1_UNC PF07738.3 −20.4 Sad1/UNC-like C-terminal Sina PF03145.7 −48.4 Seven in absentia protein family Spermine_synth PF01564.7 −93.8 Spermine/spermidine synthase Sterol_desat PF01598.8 −13 Sterol desaturase Sugar_tr PF00083.14 −85 Sugar (and other) transporter TPP_enzyme_C PF02775.11 19.7 Thiamine pyrophosphate enzyme, C- terminal TPP binding domain TPP_enzyme_M PF00205.12 −8.1 Thiamine pyrophosphate enzyme, central domain TPP_enzyme_N PF02776.8 −70 Thiamine pyrophosphate enzyme, N- terminal TPP binding domain TPR_1 PF00515.18 7.7 Tetratricopeptide repeat TPR_2 PF07719.7 20.1 Tetratricopeptide repeat TPR_4 PF07721.5 15 Tetratricopeptide repeat TPT PF03151.7 −15.3 Triose-phosphate Transporter family TP_methylase PF00590.10 −38 Tetrapyrrole (Corrin/Porphyrin) Methylases Thi4 PF01946.7 −65.1 Thi4 family Thioredoxin PF00085.10 −25.7 Thioredoxin Tim17 PF02466.9 2.7 Tim17/Tim22/Tim23 family Tryp_alpha_amyl PF00234.12 −4 Protease inhibitor/seed storage/LTP family UAA PF08449.2 −146.2 UAA transporter family VPS28 PF03997.3 25 VPS28 protein Vps4_C PF09336.1 −4.6 Vps4 C terminal oligomerisation domain WD40 PF00400.22 21.5 WD domain, G-beta repeat Whirly PF08536.2 25 Whirly transcription factor YABBY PF04690.4 25 YABBY protein YDG_SRA PF02182.8 25 YDG/SRA domain adh_short PF00106.15 −40.2 short chain dehydrogenase bZIP_1 PF00170.11 24.5 bZIP transcription factor bZIP_2 PF07716.5 15 Basic region leucine zipper eIF-1a PF01176.9 20 Translation initiation factor 1A/IF-1 efhand PF00036.22 21.7 EF hand mTERF PF02536.5 −60 mTERF p450 PF00067.12 −105 Cytochrome P450 peroxidase PF00141.13 −10 Peroxidase tRNA-synt_2 PF00152.11 −168.2 tRNA synthetases class II (D, K and N) tRNA_anti PF01336.15 8 OB-fold nucleic acid binding domain ubiquitin PF00240.13 19.4 Ubiquitin family zf-C3HC4 PF00097.15 16 Zinc finger, C3HC4 type (RING finger) zf-CCCH PF00642.15 0 Zinc finger C-x8-C-x5-C-x3-H type (and similar) zf-Dof PF02701.6 25 Dof domain, zinc finger zf-UBR PF02207.10 25 Putative zinc finger in N-recognin (UBR box)

Example 9. Selection of Transgenic Plants with Enhanced Agronomic Trait(s)

This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression of a protein selected from the group including the homologous proteins identified in Example 6. Transgenic plant cells of corn, soybean, cotton, canola, alfalfa, wheat and rice are transformed with recombinant DNA for expressing each of the homologs identified in Example 6. Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression of the homologous proteins. 

What is claimed is:
 1. A plant cell nucleus with stably integrated, recombinant DNA construct, wherein said recombinant DNA construct comprises a promoter that is functional in a plant cell and that is operably linked to a DNA segment encoding a protein comprising an amino acid sequence of SEQ ID NO: 309; and wherein said recombinant DNA construct is stably integrated into a chromosome in said plant cell nucleus which is selected by screening a population of transgenic plants that have said recombinant DNA construct and an enhanced trait as compared to control plants that do not have said recombinant DNA construct in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 2. A recombinant DNA construct comprising a promoter that is functional in a plant cell and that is operably linked to a DNA segment that encodes: a. at least one protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of zf-CCCH, PALP, GAF::HisKA::HATPase_c, TPR_2::TPR_1::TPR_2::TPR_1::TPR_4::TPR_2::TPR_1, efhand::efhand, Spermine_synth, ELFV_dehydrog_N::ELFV_dehydrog, PFK, PAS_3::PAS_3::Pkinase, S1, GDC-P, SWIM, B12-binding::Radical_SAM, 51, LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, Chloroa_b-bind, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, WD40::WD40, YABBY, Ldh_1_N::Ldh_1_C, Sina, Na_H_antiport_1, ParBc, YABBY, Histone, Fe_bilin_red, Tryp_alpha_amyl, Pyr_redox_2::Thioredoxin, E2F_TDP, CN hydrolase, YDG_SRA::Pre-SET::SET, APC8::TPR_1::TPR_1::TPR_1, Ras, tRNA_anti::tRNA-synt_2, Auxin_inducible, PGI, S1, Chloroa_b-bind, Bac_globin, Glyco_hydro_17, MGS, Spermine_synth, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Aa_trans, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_(—)1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase_Tyr, Gln-synt_N::Gln-synt_C, SAP18, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C, zf-C3HC4, eIF-1a, RPE65, PBP, Pkinase, AA_permease, F-box::LRR_1::LRR_2, zf-CCCH::zf-CCCH, Lactamase_B::Flavodoxin_1::Flavin_Reduct, Bac_globin, DSPc, adh_short, Tim17, Oxidored_molyb::Mo-co_dimer::Cyt-b5::FAD_binding_6::NAD_binding_1, ubiquitin::ubiquitin::ubiquitin::ubiquitin, MBD, CXC::CXC, HSF_DNA-bind, Spermine_synth, AP2, Peptidase_S10, PALP, EIN3, Gln-synt_N::Gln-synt_C, 2OG-FeII_Oxy, Glyco_hydro_9, GDC-P, B3, PTPA, Acyltransferase, Isochorismatase, FMO-like, Molybdop_Fe4S4::Molybdopterin::Molydop_binding::Fer2_BFD, Lir1, Prismane, Fer2, DEAD::Helicase_C, Molybdop_Fe4S4::Molybdopterin::Molydop_binding::Fer2_BFD, KNOX1::KNOX2::ELK, Glyoxalase, Sad1_UNC, Bac_globin, VPS28, PP2C, Pkinase::efhand::efhand::efhand, LEA_3, Peptidase_S10, Pkinase, CBFD_NFYB_HMF, Gln-synt_N::Gln-synt_C, Pyr_redox_2::Fer2_BFD::NIR_SIR_ferr:NIR_SIR, NUDIX::NUDIX, FAD_binding_3, GST_N::GST_C, SAM_decarbox, Acyltransferase, NTP_transferase, G-patch, 2OG-FeII_Oxy, Gln-synt_N::Gln-synt_C, AAA::Vps4_C, Histone, Pkinase, TPR_1, F-box::Kelch_1::Kelch_1, Spermine_synth, Bac_globin, Bac_globin, zf-UBR, Homeobox::HALZ, Whirly, NAD_binding_1, PTR2, EIN3, 4HBT, adh_short, 2OG-FeII_Oxy, P-II, Myb_DNA-binding::Myb_DNA-binding, DAGK_cat, AP2, MFS_1, Chloroa_b-bind, DUF716, zf-Dof, CCT, Homeobox::HALZ, Histone, 2OG-FeII_Oxy, Globin, Pyr_redox_2::Fer2_BFD::NIR_SIR_ferr:NIR_SIR, Whirly, PsbP, bZIP_1, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase_Tyr, Phi_1, BURP, Sterol_desat, DSPc, SNF5, Acyltransferase, GATase_2::Asn_synthase, adh_short, Homeobox::START, Pkinase, ParBc, SOUL, DNA_photolyase::FAD_binding_7, Pkinase_Tyr, NAD_Gly3P_dh_N::NAD_Gly3P_dh_C, Na_H_Exchanger, peroxidase, Oxidored_molyb::Mo-co_dimer::Cyt-b5::FAD_binding_6::NAD_binding_1, Hexokinase_1::Hexokinase_2, DUF716, S10_plectin, Thi4, p450, CCT, adh_short, PSI_PSAK, DUF640, Thioredoxin, Globin, Ank::Pkinase, DAGAT, RPE65, Ank::Pkinase, GSHPx, Gln-synt_N::Gln-synt_C, MtN3_slv::MtN3_slv, Allene_oxcyc, IGPD, MBD, CorA, Response_reg, Histone, AAA, Ribosomal_L10e, Pkinase, DUF26::DUF26::Pkinase, p450, mTERF, AA_kinase, PBP, GUN4, Lactamase_B::Flavodoxin_1::Rubredoxin, C2, RRM_1::RRM_1, Histone, Alpha-amylase, HLH, Thioredoxin, Histone_HNS, Myb_DNA-binding::Myb_DNA-binding, Cytochrom_C552, AP2::AP2, MtN3_slv::MtN3_slv, SWAT, ParBc, Mit_rib_S27, Ribosomal_S2, KNOX1::KNOX2::ELK, MFS_1, Glyco_transf_5::Glycos_transf_1, Cellulase, Ribosomal_L10e, Spermine_synth, Glyco_hydro_2_N::Glyco_hydro_2::Glyco_hydro_2_C, TP_methylase, AP2::AP2, Histone, Response_reg::CCT, Histone_HNS, DUF1716, p450, GATA, Pkinase, Sugar_tr, Aa_trans, Pribosyltran, Ribosomal_L10e, HLH, PMSR, DnaJ::DnaJ_CXXCXGXG::DnaJ_C, DUF1005, Glyco_transf_5::Glycos_transf_1, Spermine_synth, S1::EIF_2_alpha, RGS, Na_sulph_symp, S1, MtN3_slv::MtN3_slv, Lactamase_B::Flavin_Reduct, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Chloroa_b-bind, PTR2, Agglutinin, PLATZ, NPH3, Auxin_inducible, PTR2, GAF::HisKA::Response_reg, PsbQ, GSH_synth_ATP, GATase_2::Asn_synthase, PHP, FtsJ, DUF6::TPT, Proteasome, PsbW_2, Glyco_hydro_9, NAD_binding_2::6 PGD, S1::EIF_2_alpha, Homeobox::START::MEKHLA, S1, Isoamylase_N::Alpha-amylase, E2F_TDP, and Rieske::PaO; b. a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 30526 through 30550; c. a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NOs 352, 493, 533 and 544, and homologs thereof listed in Table 8; d. a protein having an amino acid sequence having at least 70% identity to an amino acid sequence selected from the group consisting of SEQ ID NOs 320 and 383; or e. a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 299 through SEQ ID NO: 30468; and wherein said recombinant DNA construct is stably integrated into a chromosome in a plant cell nucleus which is selected by screening a population of transgenic plants that have said recombinant DNA construct and an enhanced trait as compared to control plants that do not have said recombinant DNA construct in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 3. A transgenic plant cell nucleus comprising a recombinant DNA construct of claim
 2. 4. A transgenic plant cell having a plant cell nucleus of claim
 3. 5. The transgenic plant cell of claim 4 wherein said transgenic plant cell is homozygous for said recombinant DNA construct.
 6. The transgenic plant cell of claim 4 further comprising DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell.
 7. The transgenic plant cell of claim 5 wherein said herbicide is a glyphosate, dicamba, or glufosinate compound.
 8. A transgenic plant comprising a plurality of plant cells of claim
 4. 9. The transgenic plant of claim 8 wherein said transgenic plant is homozygous for said recombinant DNA construct.
 10. A transgenic seed comprising a recombinant DNA construct of claim
 2. 11. The transgenic seed of claim 10 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
 12. A transgenic pollen grain comprising a recombinant DNA construct of claim
 2. 13. A method for manufacturing transgenic seeds that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of a DNA segment in a plant cell nucleus comprising a recombinant DNA construct of claim 2, wherein said method comprises: (a) screening a population of plants for said enhanced trait and said recombinant DNA construct, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain said recombinant DNA construct, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil; (b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants; and (c) collecting seeds from selected plant selected from step b.
 14. The method of claim 13, wherein said method further comprises: (a) verifying that said recombinant DNA construct is stably integrated in said selected plants; and (b) analyzing tissue of said selected plant to determine the expression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of one of SEQ ID NO: 299 through SEQ ID NO:
 30468. 15. The method of claim 14 wherein said seed is corn, soybean, cotton, alfalfa, canola wheat or rice seed.
 16. A method of producing hybrid corn seed comprising: (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a stably-integrated, recombinant DNA construct of claim 2; (b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA construct, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA construct, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA construct; (c) selecting corn plants which are homozygous or hemizygous for said recombinant DNA construct by treating with an herbicide; (d) collecting seeds from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; (e) repeating steps (c) and (d) at least once to produce an inbred corn line; and (f) crossing said inbred corn line with a second corn line to produce hybrid corn seed. 